Summary
Next Generation Sequencing
Debian Med bioinformatics applications usable in Next Generation Sequencing
It aims at gettting packages which specialize in the processing or interpretation of
data generated with next- (and later-) generation high-thoughput sequencing technologies.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Med
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Med mailing list
Links to other tasks
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Debian Med Next Generation Sequencing packages
Official Debian packages with high relevance
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anfo
??? missing short description for package anfo :-(
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| Versions of package anfo |
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| Release | Version | Architectures |
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| bullseye | 0.98-8 | amd64,arm64,armhf,i386 |
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License: DFSG free
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arden
??? missing short description for package arden :-(
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| Versions of package arden |
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| Release | Version | Architectures |
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| sid | 1.0-6 | all |
| bullseye | 1.0-5 | all |
| bookworm | 1.0-5 | all |
| trixie | 1.0-6 | all |
| forky | 1.0-6 | all |
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License: DFSG free
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art-nextgen-simulation-tools
??? missing short description for package art-nextgen-simulation-tools :-(
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| Versions of package art-nextgen-simulation-tools |
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| Release | Version | Architectures |
|---|
| bullseye | 20160605+dfsg-4 | amd64,arm64,armhf,i386 |
| sid | 20160605+dfsg-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 20160605+dfsg-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 20160605+dfsg-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 20160605+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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artfastqgenerator
??? missing short description for package artfastqgenerator :-(
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| Versions of package artfastqgenerator |
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| Release | Version | Architectures |
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| bookworm | 0.0.20150519-4 | all |
| trixie | 0.0.20150519-5 | all |
| forky | 0.0.20150519-6 | all |
| sid | 0.0.20150519-6 | all |
| bullseye | 0.0.20150519-4 | all |
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License: DFSG free
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bamtools
??? missing short description for package bamtools :-(
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| Versions of package bamtools |
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| Release | Version | Architectures |
|---|
| forky | 2.5.3+dfsg-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 2.5.1+dfsg-9 | amd64,arm64,armhf,i386 |
| bookworm | 2.5.2+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 2.5.2+dfsg-6 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| sid | 2.5.3+dfsg-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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bcftools
??? missing short description for package bcftools :-(
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| Versions of package bcftools |
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| Release | Version | Architectures |
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| trixie | 1.21-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 1.11-1 | amd64,arm64,armhf,i386 |
| bookworm | 1.16-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| forky | 1.22-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.22-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| upstream | 1.23.1 |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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bedtools
??? missing short description for package bedtools :-(
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| Versions of package bedtools |
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| Release | Version | Architectures |
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| forky | 2.31.1+dfsg-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.31.1+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 2.30.0+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.30.0+dfsg-1 | amd64,arm64,armhf,i386 |
| sid | 2.31.1+dfsg-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| Debtags of package bedtools: |
|---|
| field | biology, biology:bioinformatics |
| interface | commandline |
| role | program |
| scope | suite |
| use | analysing, comparing, converting, filtering |
| works-with | biological-sequence |
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License: DFSG free
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berkeley-express
??? missing short description for package berkeley-express :-(
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| Versions of package berkeley-express |
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| Release | Version | Architectures |
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| bookworm | 1.5.3+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.5.3+dfsg-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 1.5.3+dfsg-1 | amd64,arm64,armhf,i386 |
| forky | 1.5.3+dfsg-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.5.3+dfsg-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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bio-rainbow
??? missing short description for package bio-rainbow :-(
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| Versions of package bio-rainbow |
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| Release | Version | Architectures |
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| bullseye | 2.0.4+dfsg-2 | amd64,arm64,armhf,i386 |
| sid | 2.0.4+dfsg-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 2.0.4+dfsg-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 2.0.4+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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blasr
??? missing short description for package blasr :-(
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| Versions of package blasr |
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| Release | Version | Architectures |
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| sid | 5.3.5+dfsg-8 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 5.3.5+dfsg-7 | amd64,arm64,ppc64el,riscv64 |
| forky | 5.3.5+dfsg-8 | amd64,arm64,ppc64el,riscv64 |
| bullseye | 5.3.3+dfsg-5 | amd64,arm64 |
| bookworm | 5.3.5+dfsg-6 | amd64,arm64,mips64el,ppc64el |
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License: DFSG free
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bowtie
??? missing short description for package bowtie :-(
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| Versions of package bowtie |
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| Release | Version | Architectures |
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| forky | 1.3.1-3 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| bookworm | 1.3.1-1 | amd64,arm64,mips64el,ppc64el,s390x |
| sid | 1.3.1-3 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| bullseye | 1.3.0+dfsg1-1 | amd64,arm64 |
| trixie | 1.3.1-3 | amd64,arm64,ppc64el,riscv64,s390x |
| Debtags of package bowtie: |
|---|
| biology | nuceleic-acids |
| field | biology:bioinformatics |
| interface | commandline |
| role | program |
| science | calculation |
| scope | utility |
| use | analysing, comparing |
| works-with | biological-sequence |
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License: DFSG free
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bowtie2
??? missing short description for package bowtie2 :-(
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| Versions of package bowtie2 |
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| Release | Version | Architectures |
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| forky | 2.5.5-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| sid | 2.5.5-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| bookworm | 2.5.0-3 | amd64,arm64,mips64el,ppc64el |
| trixie | 2.5.4-1 | amd64,arm64,ppc64el,riscv64 |
| bullseye | 2.4.2-2 | amd64,arm64 |
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License: DFSG free
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bwa
??? missing short description for package bwa :-(
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| Versions of package bwa |
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| Release | Version | Architectures |
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| sid | 0.7.19-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 0.7.17-6 | amd64,arm64,armhf,i386 |
| forky | 0.7.19-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.7.18-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.7.17-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| Debtags of package bwa: |
|---|
| biology | nuceleic-acids, peptidic |
| field | biology, biology:bioinformatics |
| interface | commandline, text-mode |
| role | program |
| use | analysing, comparing |
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License: DFSG free
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canu
??? missing short description for package canu :-(
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| Versions of package canu |
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| Release | Version | Architectures |
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| sid | 2.2+dfsg-5 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| bookworm | 2.0+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.0+dfsg-1 | amd64,arm64,armhf,i386 |
| upstream | 2.3 |
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License: DFSG free
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changeo
??? missing short description for package changeo :-(
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| Versions of package changeo |
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| Release | Version | Architectures |
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| bookworm | 1.3.0-1 | all |
| forky | 1.3.0-4 | all |
| trixie | 1.3.0-3 | all |
| sid | 1.3.0-4 | all |
| bullseye | 1.0.2-1 | all |
| upstream | 1.3.4 |
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License: DFSG free
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Please cite:
Namita T. Gupta, Jason A. Vander Heiden, Mohamed Uduman, Daniel Gadala-Maria, Gur Yaari and Steven H. Kleinstein:
Link
to publication
(PubMed,eprint)
Bioinformatics
31(20):3356-3358
(2015)
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crac
??? missing short description for package crac :-(
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| Versions of package crac |
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| Release | Version | Architectures |
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| sid | 2.5.2+dfsg-7 | amd64,arm64,loong64,ppc64el,riscv64 |
| bookworm | 2.5.2+dfsg-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el |
| trixie | 2.5.2+dfsg-6 | amd64,arm64,ppc64el,riscv64 |
| bullseye | 2.5.2+dfsg-4 | amd64,arm64,armhf,i386 |
| forky | 2.5.2+dfsg-7 | amd64,arm64,loong64,ppc64el,riscv64 |
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License: DFSG free
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cutadapt
??? missing short description for package cutadapt :-(
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| Versions of package cutadapt |
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| Release | Version | Architectures |
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| trixie | 4.7-2 | all |
| forky | 4.7-2 | all |
| sid | 4.7-2 | all |
| bullseye | 3.2-2 | all |
| bookworm | 4.2-1 | all |
| upstream | 5.2 |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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daligner
??? missing short description for package daligner :-(
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| Versions of package daligner |
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| Release | Version | Architectures |
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| trixie | 1.0+git20240119.335105d-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.0+git20221215.bd26967-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1.0+git20200727.ed40ce5-3 | amd64,arm64,armhf,i386 |
| sid | 1.0+git20240119.335105d-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.0+git20240119.335105d-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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deepnano
??? missing short description for package deepnano :-(
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| Versions of package deepnano |
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| Release | Version | Architectures |
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| bullseye | 0.0+git20170813.e8a621e-3.1 | amd64,arm64,armhf,i386 |
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License: DFSG free
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discosnp
??? missing short description for package discosnp :-(
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| Versions of package discosnp |
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| Release | Version | Architectures |
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| sid | 2.6.2-5 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 4.4.4-1 | amd64,arm64,i386 |
| bookworm | 2.6.2-2 | amd64,arm64,mips64el,ppc64el |
| trixie | 2.6.2-4 | amd64,arm64,ppc64el,riscv64 |
| forky | 2.6.2-5 | amd64,arm64,ppc64el,riscv64 |
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License: DFSG free
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dnaclust
??? missing short description for package dnaclust :-(
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| Versions of package dnaclust |
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| Release | Version | Architectures |
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| bookworm | 3-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 3-7 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| sid | 3-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 3-7 | amd64,arm64,armhf,i386 |
| forky | 3-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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dwgsim
??? missing short description for package dwgsim :-(
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| Versions of package dwgsim |
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| Release | Version | Architectures |
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| bookworm | 0.1.14-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 0.1.14-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 0.1.14-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.1.14-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 0.1.12-4 | amd64,arm64,armhf,i386 |
| upstream | 0.1.16 |
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License: DFSG free
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ea-utils
??? missing short description for package ea-utils :-(
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| Versions of package ea-utils |
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| Release | Version | Architectures |
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| bullseye | 1.1.2+dfsg-6 | amd64,arm64,armhf,i386 |
| bookworm | 1.1.2+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.1.2+dfsg-9 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| sid | 1.1.2+dfsg-10 | amd64,arm64,loong64,ppc64el,riscv64 |
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License: DFSG free
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fastaq
??? missing short description for package fastaq :-(
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| Versions of package fastaq |
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| Release | Version | Architectures |
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| sid | 3.17.0-9 | all |
| bullseye | 3.17.0-3 | all |
| bookworm | 3.17.0-5 | all |
| trixie | 3.17.0-9 | all |
| forky | 3.17.0-9 | all |
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License: DFSG free
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fastp
??? missing short description for package fastp :-(
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| Versions of package fastp |
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| Release | Version | Architectures |
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| bullseye | 0.20.1+dfsg-1 | amd64,arm64,armhf,i386 |
| forky | 1.0.1+dfsg-1 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| sid | 1.0.1+dfsg-1 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| trixie | 0.24.0+dfsg-1 | amd64,arm64,ppc64el,riscv64,s390x |
| bookworm | 0.23.2+dfsg-2 | amd64,arm64,armel,armhf,mips64el,mipsel,ppc64el,s390x |
| upstream | 1.3.3 |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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fastqc
??? missing short description for package fastqc :-(
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| Versions of package fastqc |
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| Release | Version | Architectures |
|---|
| trixie | 0.12.1+dfsg-4 | all |
| bullseye | 0.11.9+dfsg-4 | all |
| sid | 0.12.1+dfsg-4 | all |
| forky | 0.12.1+dfsg-4 | all |
| bookworm | 0.11.9+dfsg-6 | all |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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flexbar
??? missing short description for package flexbar :-(
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| Versions of package flexbar |
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| Release | Version | Architectures |
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| bullseye | 3.5.0-3 | amd64,arm64,armhf,i386 |
| sid | 3.5.0-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 3.5.0-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 3.5.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 3.5.0-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
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License: DFSG free
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The package is enhanced by the following packages:
multiqc
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fml-asm
??? missing short description for package fml-asm :-(
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| Versions of package fml-asm |
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| Release | Version | Architectures |
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| bullseye | 0.1+git20190320.b499514-1 | amd64,arm64,armhf,i386 |
| sid | 0.1+git20221215.85f159e-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 0.1+git20221215.85f159e-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.1+git20221215.85f159e-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.1+git20190320.b499514-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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fsm-lite
??? missing short description for package fsm-lite :-(
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| Versions of package fsm-lite |
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| Release | Version | Architectures |
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| trixie | 1.0-8 | amd64,arm64,ppc64el,riscv64,s390x |
| bullseye | 1.0-5 | amd64,arm64 |
| bookworm | 1.0-8 | amd64,arm64,mips64el,ppc64el,s390x |
| forky | 1.0-8 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| sid | 1.0-8 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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grinder
??? missing short description for package grinder :-(
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| Versions of package grinder |
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| Release | Version | Architectures |
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| sid | 0.5.4-6 | all |
| forky | 0.5.4-6 | all |
| trixie | 0.5.4-6 | all |
| bookworm | 0.5.4-6 | all |
| bullseye | 0.5.4-6 | all |
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License: DFSG free
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hilive
??? missing short description for package hilive :-(
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| Versions of package hilive |
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| Release | Version | Architectures |
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| sid | 2.0a-6 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 2.0a-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.0a-3 | amd64,arm64,armhf,i386 |
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License: DFSG free
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hinge
??? missing short description for package hinge :-(
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| Versions of package hinge |
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| Release | Version | Architectures |
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| bullseye | 0.5.0-6 | amd64,arm64,armhf,i386 |
| bookworm | 0.5.0-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| trixie | 0.5.0-7 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| sid | 0.5.0-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
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License: DFSG free
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hisat2
??? missing short description for package hisat2 :-(
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| Versions of package hisat2 |
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| Release | Version | Architectures |
|---|
| forky | 2.2.1-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.2.1-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 2.2.1-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.2.1-2 | amd64,arm64,armhf,i386 |
| sid | 2.2.1-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| upstream | 2.2.2 |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
idba
??? missing short description for package idba :-(
|
| Versions of package idba |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.1.3-7 | amd64,arm64,armhf,i386 |
| trixie | 1.1.3-8 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| forky | 1.1.3-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.1.3-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
igor
??? missing short description for package igor :-(
|
| Versions of package igor |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.4.0+dfsg-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 1.4.0+dfsg-2 | amd64,arm64,armhf,i386 |
| sid | 1.4.0+dfsg-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.4.0+dfsg-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 1.4.0+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
igv
??? missing short description for package igv :-(
|
| Versions of package igv |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2.16.0+dfsg-1 | all |
| sid | 2.18.5+dfsg-4 | all |
| bullseye | 2.6.3+dfsg-3 (non-free) | all |
| trixie | 2.18.5+dfsg-1 | all |
| upstream | 2.19.7 |
| Debtags of package igv: |
|---|
| field | biology |
| interface | x11 |
| network | client |
| role | program |
| scope | utility |
| use | viewing |
| works-with | biological-sequence |
|
License: DFSG free
|
Please cite:
James T Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S Lander, Gad Getz and Jill P Mesirov:
Integrative genomics viewer.
(PubMed,eprint)
Nature Biotechnology
29(1):24–26
(2011)
|
|
|
iva
??? missing short description for package iva :-(
|
| Versions of package iva |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.0.11+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| bullseye | 1.0.9+ds-11 | amd64,arm64,armhf,i386 |
| trixie | 1.0.11+ds-6 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| forky | 1.0.11+ds-6 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| sid | 1.0.11+ds-6 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
|
License: DFSG free
|
|
|
|
|
khmer
??? missing short description for package khmer :-(
|
| Versions of package khmer |
|---|
| Release | Version | Architectures |
|---|
| experimental | 3.0.0~a3+dfsg-9~0exp | amd64 |
| bookworm | 3.0.0~a3+dfsg-4 | amd64 |
| bullseye | 2.1.2+dfsg-8 | amd64,arm64 |
|
License: DFSG free
|
Please cite:
Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Bucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela McA'Nulty, Eric McDonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N Russ, Erich Schwarz, Camille Scott, Josiah Seaman, Scott Sievert, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Joe Stein, Susan R Steinman, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, en zyme and C. Titus Brown:
The khmer software package: enabling efficient sequence analysis.
(2015)
|
|
|
kissplice
??? missing short description for package kissplice :-(
|
| Versions of package kissplice |
|---|
| Release | Version | Architectures |
|---|
| forky | 2.6.7-2 | amd64,arm64,ppc64el,riscv64 |
| bookworm | 2.6.2-2 | amd64,arm64,mips64el,ppc64el |
| bullseye | 2.5.3-3 | amd64,arm64 |
| sid | 2.6.7-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 2.6.7-2 | amd64,arm64,ppc64el,riscv64 |
| Debtags of package kissplice: |
|---|
| biology | nuceleic-acids |
| field | biology, biology:bioinformatics |
| interface | commandline |
| role | program |
| use | analysing |
| works-with | biological-sequence |
|
License: DFSG free
|
Topics: RNA-seq; RNA splicing; Gene structure
|
|
|
kraken
??? missing short description for package kraken :-(
|
| Versions of package kraken |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.1.1-4 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 1.1.1-4 | amd64,arm64,ppc64el,riscv64 |
| bullseye | 1.1.1-2 | amd64,arm64,armhf,i386 |
| bookworm | 1.1.1-4 | amd64,arm64,mips64el,ppc64el |
| forky | 1.1.1-4 | amd64,arm64,loong64,ppc64el,riscv64 |
|
License: DFSG free
|
|
|
|
|
kraken2
??? missing short description for package kraken2 :-(
|
| Versions of package kraken2 |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2.1.2-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.1.1-1 | amd64,arm64,armhf,i386 |
| forky | 2.1.3-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.1.3-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| sid | 2.1.3-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| upstream | 2.17.1 |
|
License: DFSG free
|
|
|
|
|
last-align
??? missing short description for package last-align :-(
|
| Versions of package last-align |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1609-1 | amd64,arm64,ppc64el,riscv64,s390x |
| bookworm | 1447-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1179-1 | amd64,arm64,armhf,i386 |
| sid | 1651-2 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| forky | 1651-2 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| Debtags of package last-align: |
|---|
| biology | nuceleic-acids |
| field | biology, biology:bioinformatics |
| role | program |
|
License: DFSG free
|
|
|
|
|
libvcflib-tools
??? missing short description for package libvcflib-tools :-(
|
| Versions of package libvcflib-tools |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.0.12+dfsg-1 | amd64,arm64,ppc64el,riscv64 |
| bookworm | 1.0.3+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| forky | 1.0.12+dfsg-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| sid | 1.0.12+dfsg-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 1.0.2+dfsg-2 | amd64,arm64,armhf,i386 |
| upstream | 1.0.15 |
|
License: DFSG free
|
|
|
|
|
macs
??? missing short description for package macs :-(
|
| Versions of package macs |
|---|
| Release | Version | Architectures |
|---|
| trixie | 3.0.2-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 2.2.7.1-6 | amd64,arm64,armel,armhf,i386,ppc64el,s390x |
| bullseye | 2.2.7.1-3 | amd64,arm64,armhf,i386 |
| sid | 3.0.4-1 | amd64,arm64,loong64,ppc64el |
| sid | 3.0.2-3 | armhf,i386,riscv64,s390x |
| forky | 3.0.2-3 | amd64,arm64,armhf,i386,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Please cite:
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S. Johnson, Bradley E. Bernstein, Chad Nussbaum, Richard M. Myers, Myles Brown, Wei Li and X Shirley Liu:
Model-based Analysis of ChIP-Seq (MACS).
(PubMed,eprint)
Genome Biol.
9(9):R137
(2008)
|
|
|
mapdamage
??? missing short description for package mapdamage :-(
|
| Versions of package mapdamage |
|---|
| Release | Version | Architectures |
|---|
| trixie | 2.2.2+dfsg-1 | all |
| bullseye | 2.2.1+dfsg-1 | all |
| sid | 2.2.3+dfsg-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| bookworm | 2.2.1+dfsg-3 | all |
|
License: DFSG free
|
|
|
|
|
mapsembler2
??? missing short description for package mapsembler2 :-(
|
| Versions of package mapsembler2 |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.2.4+dfsg1-3 | amd64,arm64 |
| bookworm | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
| trixie | 2.2.4+dfsg1-4 | amd64,arm64,ppc64el,s390x |
| sid | 2.2.4+dfsg1-6 | amd64,arm64,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
maq
??? missing short description for package maq :-(
|
| Versions of package maq |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.7.1-9 | amd64,arm64,armhf,i386 |
| forky | 0.7.1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 0.7.1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.7.1-10 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.7.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| Debtags of package maq: |
|---|
| biology | nuceleic-acids |
| field | biology, biology:bioinformatics |
| interface | commandline |
| role | program |
| scope | utility |
| use | analysing, comparing, searching |
| works-with-format | plaintext |
|
License: DFSG free
|
|
|
|
|
maqview
??? missing short description for package maqview :-(
|
| Versions of package maqview |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 0.2.5-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 0.2.5-10 | amd64,arm64,armhf,i386 |
| sid | 0.2.5-12 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 0.2.5-12 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.2.5-12 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
mhap
??? missing short description for package mhap :-(
|
| Versions of package mhap |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2.1.3+dfsg-3 | all |
| sid | 2.1.3+dfsg-3 | all |
| forky | 2.1.3+dfsg-3 | all |
| bullseye | 2.1.3+dfsg-3 | all |
| trixie | 2.1.3+dfsg-3 | all |
|
License: DFSG free
|
|
|
|
|
microbiomeutil
??? missing short description for package microbiomeutil :-(
|
| Versions of package microbiomeutil |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 20101212+dfsg1-4 | all |
| sid | 20101212+dfsg1-6 | all |
| bookworm | 20101212+dfsg1-5 | all |
| trixie | 20101212+dfsg1-6 | all |
| forky | 20101212+dfsg1-6 | all |
|
License: DFSG free
|
Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
|
|
|
mira-assembler
??? missing short description for package mira-assembler :-(
|
| Versions of package mira-assembler |
|---|
| Release | Version | Architectures |
|---|
| sid | 4.9.6-12 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 4.9.6-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 4.9.6-5 | amd64,arm64,armhf,i386 |
| forky | 4.9.6-12 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 4.9.6-11 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| Debtags of package mira-assembler: |
|---|
| role | program |
|
License: DFSG free
|
|
|
|
|
mothur
??? missing short description for package mothur :-(
|
| Versions of package mothur |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.48.1-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 1.44.3-2 | amd64,arm64,armhf,i386 |
| forky | 1.48.5-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.48.5-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 1.48.0-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| Debtags of package mothur: |
|---|
| role | program |
|
License: DFSG free
|
Please cite:
Patrick D Schloss, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, Brian B Oakley, Donovan H Parks, Courtney J Robinson, Jason W Sahl, Blaz Stres, Gerhard G Thallinger, David J Van Horn and Carolyn F Weber:
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities.
(PubMed)
Appl Environ Microbiol
75(23):7537-7541
(2009)
Topics: Microbial ecology
|
|
|
nanopolish
??? missing short description for package nanopolish :-(
|
| Versions of package nanopolish |
|---|
| Release | Version | Architectures |
|---|
| forky | 0.14.0-2 | amd64,arm64,armhf,i386,ppc64el,riscv64 |
| sid | 0.14.0-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| bullseye | 0.13.2-3 | amd64,arm64,armhf,i386 |
| bookworm | 0.14.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| trixie | 0.14.0-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
|
License: DFSG free
|
|
|
|
|
paleomix
??? missing short description for package paleomix :-(
|
| Versions of package paleomix |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.3.7-3 | amd64,arm64 |
| sid | 1.3.10-1 | amd64,arm64 |
| bullseye | 1.3.2-1 | amd64,arm64 |
| trixie | 1.3.8-2 | amd64,arm64 |
| upstream | 1.4.0 |
|
License: DFSG free
|
Please cite:
Mikkel Schubert, Luca Ermini, Clio Der Sarkissian, Hákon Jónsson, Aurélien Ginolhac, Robert Schaefer, Michael D Martin, Ruth Fernández, Martin Kircher, Molly McCue, Eske Willerslev and Ludovic Orlando:
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
(PubMed)
Nature Protocols
9(5):1056-82
(2014)
|
|
|
pbhoney
??? missing short description for package pbhoney :-(
|
| Versions of package pbhoney |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 15.8.24+dfsg-7 | all |
| bullseye | 15.8.24+dfsg-7 | all |
| sid | 15.8.24+dfsg-8 | all |
|
License: DFSG free
|
|
|
|
|
pbjelly
??? missing short description for package pbjelly :-(
|
| Versions of package pbjelly |
|---|
| Release | Version | Architectures |
|---|
| sid | 15.8.24+dfsg-8 | all |
| bookworm | 15.8.24+dfsg-7 | all |
| bullseye | 15.8.24+dfsg-7 | all |
|
License: DFSG free
|
|
|
|
|
pbsuite
??? missing short description for package pbsuite :-(
|
| Versions of package pbsuite |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 15.8.24+dfsg-7 | all |
| bookworm | 15.8.24+dfsg-7 | all |
| sid | 15.8.24+dfsg-8 | all |
|
License: DFSG free
|
|
|
|
|
picard-tools
??? missing short description for package picard-tools :-(
|
| Versions of package picard-tools |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.24.1+dfsg-1 | all |
| bookworm | 2.27.5+dfsg-2 | all |
| trixie | 3.3.0+dfsg-2 | all |
| forky | 3.4.0+dfsg-1 | all |
| sid | 3.4.0+dfsg-1 | all |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
Please cite:
Broad Institute:
Picard toolkit.
Broad Institute, GitHub repository
(2019)
Topics: Sequencing; Document, record and content management
|
|
|
pirs
??? missing short description for package pirs :-(
|
| Versions of package pirs |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.0.2+dfsg-9 | amd64,arm64,armhf,i386 |
| forky | 2.0.2+dfsg-13 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 2.0.2+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 2.0.2+dfsg-12 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| sid | 2.0.2+dfsg-13 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Please cite:
Xuesong Hu, Jianying Yuan, Yujian Shi, Jianliang Lu, Binghang Liu, Zhenyu Li, Yanxiang Chen, Desheng Mu, Hao Zhang, Nan Li, Zhen Yue, Fan Bai, Heng Li and Wei Fan:
pIRS: Profile-based Illumina pair-end reads simulator.
(PubMed,eprint)
Bioinformatics
28(11):1533-5
(2012)
|
|
|
pizzly
??? missing short description for package pizzly :-(
|
| Versions of package pizzly |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.37.3+ds-12 | amd64,arm64,loong64,ppc64el,riscv64,s390x |
| bullseye | 0.37.3+ds-5 | amd64,arm64,armhf,i386 |
| trixie | 0.37.3+ds-9 | amd64,arm64,ppc64el,riscv64,s390x |
| bookworm | 0.37.3+ds-9 | amd64,arm64,mips64el,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
placnet
??? missing short description for package placnet :-(
|
| Versions of package placnet |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.04-1 | all |
| trixie | 1.04-1 | all |
| bullseye | 1.03-3 | all |
| sid | 1.04-1 | all |
| forky | 1.04-1 | all |
|
License: DFSG free
|
|
|
|
|
poretools
??? missing short description for package poretools :-(
|
| Versions of package poretools |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.6.0+dfsg-7 | all |
| bullseye | 0.6.0+dfsg-5 | all |
| bookworm | 0.6.0+dfsg-6 | all |
| trixie | 0.6.0+dfsg-7 | all |
| forky | 0.6.0+dfsg-7 | all |
|
License: DFSG free
|
|
|
|
|
python3-airr
??? missing short description for package python3-airr :-(
|
| Versions of package python3-airr |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.5.1-1 | all |
| bullseye | 1.3.1-1 | all |
| sid | 1.5.1-2 | all |
| forky | 1.5.1-2 | all |
| bookworm | 1.3.1-1 | all |
| upstream | 1.6.1 |
|
License: DFSG free
|
|
|
|
|
python3-gffutils
??? missing short description for package python3-gffutils :-(
|
| Versions of package python3-gffutils |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.10.1-2 | all |
| bookworm | 0.11.1-3 | all |
| trixie | 0.13-2 | all |
| forky | 0.13-5 | all |
| sid | 0.13-5 | all |
| upstream | 0.14 |
|
License: DFSG free
|
|
|
|
|
python3-presto
??? missing short description for package python3-presto :-(
|
| Versions of package python3-presto |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.6.2-1 | all |
| forky | 0.7.6-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 0.7.6-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 0.7.1-1 | all |
| trixie | 0.7.2-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| upstream | 0.7.9 |
|
License: DFSG free
|
|
|
|
|
python3-pybedtools
??? missing short description for package python3-pybedtools :-(
|
| Versions of package python3-pybedtools |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.8.0-5 | amd64,arm64,armhf,i386 |
| forky | 0.10.0-6 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| bookworm | 0.9.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| sid | 0.10.0-6 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| trixie | 0.10.0-4 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| upstream | 0.12.0 |
|
License: DFSG free
|
|
|
|
|
python3-sqt
??? missing short description for package python3-sqt :-(
|
| Versions of package python3-sqt |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.8.0-9 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| bullseye | 0.8.0-4 | amd64,arm64,armhf,i386 |
| bookworm | 0.8.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
| trixie | 0.8.0-9 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| forky | 0.8.0-9 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
|
License: DFSG free
|
|
|
|
|
q2cli
??? missing short description for package q2cli :-(
|
| Versions of package q2cli |
|---|
| Release | Version | Architectures |
|---|
| sid | 2024.5.0-2 | all |
| bullseye | 2020.11.1-1 | all |
| bookworm | 2022.11.1-2 | all |
| upstream | 2026.4.0 |
|
License: DFSG free
|
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(eprint)
Nature Biotechnology
37
(2019)
|
|
|
qcumber
??? missing short description for package qcumber :-(
|
| Versions of package qcumber |
|---|
| Release | Version | Architectures |
|---|
| sid | 2.3.0-3 | all |
| bookworm | 2.3.0-2 | all |
| trixie | 2.3.0-2 | all |
| bullseye | 2.3.0-2 | all |
|
License: DFSG free
|
|
|
|
|
qiime
??? missing short description for package qiime :-(
|
| Versions of package qiime |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2022.11.1-2 | all |
| sid | 2024.5.0-1 | all |
| bullseye | 2020.11.1-1 | all |
| upstream | 2026.4.0 |
| Debtags of package qiime: |
|---|
| role | program |
|
License: DFSG free
|
Please cite:
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric J Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodríguez, John Chase, Emily Cope, Ricardo Da Silva, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan Holmes, Hannes Holste, Curtis Huttenhower, Gavin Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin Kaehler, Kyo Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan GI Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine Lozupone, Massoud Maher, Clarisse Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam Rivers, Michael S Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin JJ van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Chase HD Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight and J Gregory Caporaso:
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
(PubMed,eprint)
Nature Biotechnology
37:852 - 857
(2019)
Topics: Microbial ecology
|
|
|
quorum
??? missing short description for package quorum :-(
|
| Versions of package quorum |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.1.1-4 | amd64,arm64 |
| trixie | 1.1.2-2 | amd64,arm64,ppc64el,riscv64 |
| forky | 1.1.2-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| sid | 1.1.2-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| bookworm | 1.1.1-7 | amd64,arm64,mips64el,ppc64el |
|
License: DFSG free
|
|
|
|
|
r-bioc-deseq2
??? missing short description for package r-bioc-deseq2 :-(
|
| Versions of package r-bioc-deseq2 |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.46.0+dfsg-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 1.30.1+dfsg-1 | amd64,arm64,armhf,i386 |
| trixie | 1.46.0+dfsg-2 | amd64,arm64,ppc64el,riscv64,s390x |
| bookworm | 1.38.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| upstream | 1.52.0 |
|
License: DFSG free
|
|
|
|
|
r-bioc-edger
??? missing short description for package r-bioc-edger :-(
|
| Versions of package r-bioc-edger |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 3.40.2+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 4.4.2+dfsg-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 3.32.1+dfsg-1 | amd64,arm64,armhf,i386 |
| trixie | 4.4.2+dfsg-1 | amd64,arm64,ppc64el,riscv64,s390x |
| upstream | 4.10.0 |
|
License: DFSG free
|
|
|
|
|
r-bioc-hilbertvis
??? missing short description for package r-bioc-hilbertvis :-(
|
| Versions of package r-bioc-hilbertvis |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.56.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.64.0-2 | amd64,arm64,ppc64el,riscv64,s390x |
| sid | 1.64.0-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 1.48.0-1 | amd64,arm64,armhf,i386 |
| upstream | 1.70.0 |
| Debtags of package r-bioc-hilbertvis: |
|---|
| biology | nuceleic-acids |
| field | biology, biology:bioinformatics |
| use | analysing |
|
License: DFSG free
|
|
|
|
|
r-bioc-metagenomeseq
??? missing short description for package r-bioc-metagenomeseq :-(
|
| Versions of package r-bioc-metagenomeseq |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.48.1-2 | all |
| bullseye | 1.32.0-1 | all |
| bookworm | 1.40.0-1 | all |
| trixie | 1.48.1-1 | all |
| upstream | 1.54.0 |
|
License: DFSG free
|
|
|
|
|
r-bioc-rsubread
??? missing short description for package r-bioc-rsubread :-(
|
| Versions of package r-bioc-rsubread |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.4.2-1 | amd64,arm64 |
| trixie | 2.20.0-2 | amd64,arm64,ppc64el,riscv64,s390x |
| bookworm | 2.12.2-1 | amd64,arm64,mips64el,ppc64el,s390x |
| sid | 2.20.0-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| upstream | 2.26.0 |
|
License: DFSG free
|
|
|
|
|
r-cran-alakazam
??? missing short description for package r-cran-alakazam :-(
|
| Versions of package r-cran-alakazam |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.4.3-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| bookworm | 1.2.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.3.0-1 | amd64,arm64,ppc64el,riscv64,s390x |
| experimental | 1.3.0-2~0exp0 | amd64,arm64,ppc64el,riscv64,s390x |
| bullseye | 1.1.0-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
|
|
|
|
r-cran-shazam
??? missing short description for package r-cran-shazam :-(
|
| Versions of package r-cran-shazam |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.2.0-1 | all |
| bookworm | 1.1.2-1 | all |
| bullseye | 1.0.2-1 | all |
| sid | 1.3.2-1 | all |
|
License: DFSG free
|
|
|
|
|
r-cran-tcr
??? missing short description for package r-cran-tcr :-(
|
| Versions of package r-cran-tcr |
|---|
| Release | Version | Architectures |
|---|
| trixie | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 2.3.2+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 2.3.2+ds-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
|
|
|
|
r-cran-tigger
??? missing short description for package r-cran-tigger :-(
|
| Versions of package r-cran-tigger |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.0.1-1 | all |
| bullseye | 1.0.0-1 | all |
| sid | 1.1.3-1 | all |
| trixie | 1.1.0-1 | all |
|
License: DFSG free
|
|
|
|
|
rna-star
??? missing short description for package rna-star :-(
|
| Versions of package rna-star |
|---|
| Release | Version | Architectures |
|---|
| sid | 2.7.11b+dfsg-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| forky | 2.7.11b+dfsg-2 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 2.7.11b+dfsg-2 | amd64,arm64,ppc64el,riscv64 |
| bookworm | 2.7.10b+dfsg-2 | amd64,arm64,mips64el,ppc64el |
| bullseye | 2.7.8a+dfsg-2 | amd64,arm64 |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
Topics: Sequence analysis
|
|
|
rtax
??? missing short description for package rtax :-(
|
| Versions of package rtax |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.984-8 | all |
| bullseye | 0.984-7 | all |
| bookworm | 0.984-8 | all |
| trixie | 0.984-8 | all |
| forky | 0.984-8 | all |
|
License: DFSG free
|
|
|
|
|
salmon
??? missing short description for package salmon :-(
|
| Versions of package salmon |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.10.3+ds1-3 | amd64,arm64 |
| bullseye | 1.4.0+ds1-1 | amd64,arm64 |
| forky | 1.10.3+ds1-3 | amd64,arm64 |
| trixie | 1.10.2+ds1-1 | amd64,arm64 |
| bookworm | 1.10.1+ds1-1 | amd64,arm64 |
| upstream | 1.11.4 |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
sambamba
??? missing short description for package sambamba :-(
|
| Versions of package sambamba |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.0+dfsg-1 | amd64,arm64 |
| trixie | 1.0.1+dfsg-2 | amd64,arm64,riscv64 |
| bullseye | 0.8.0-1 | amd64,arm64 |
| sid | 1.0.1+dfsg-3 | amd64,arm64,riscv64 |
|
License: DFSG free
|
|
|
|
|
samblaster
??? missing short description for package samblaster :-(
|
| Versions of package samblaster |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.1.26-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 0.1.26-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.1.26-4 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.1.26-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 0.1.26-1 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
samtools
??? missing short description for package samtools :-(
|
| Versions of package samtools |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.11-1 | amd64,arm64,armhf,i386 |
| bookworm | 1.16.1-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 1.22.1-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.22.1-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 1.21-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| upstream | 1.23.1 |
| Debtags of package samtools: |
|---|
| field | biology |
| interface | commandline |
| network | client |
| role | program |
| scope | utility |
| uitoolkit | ncurses |
| use | analysing, calculating, filtering |
| works-with | biological-sequence |
|
License: DFSG free
|
|
|
|
|
scoary
??? missing short description for package scoary :-(
|
| Versions of package scoary |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.6.16-5 | all |
| trixie | 1.6.16-10 | all |
| bullseye | 1.6.16-2 | all |
| sid | 1.6.16-10 | all |
|
License: DFSG free
|
|
|
|
|
scythe
??? missing short description for package scythe :-(
|
| Versions of package scythe |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.994+git20141017.20d3cff-3 | amd64,arm64,armhf,i386 |
| forky | 0.994+git20141017.20d3cff-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.994+git20141017.20d3cff-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.994+git20141017.20d3cff-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 0.994+git20141017.20d3cff-5 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
seqprep
??? missing short description for package seqprep :-(
|
| Versions of package seqprep |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.3.2-5 | amd64,arm64,armhf,i386 |
| bookworm | 1.3.2-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.3.2-9 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 1.3.2-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.3.2-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
seqtk
??? missing short description for package seqtk :-(
|
| Versions of package seqtk |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.4-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 1.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1.3-2 | amd64,arm64,armhf,i386 |
| trixie | 1.4-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 1.4-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| upstream | 1.5 |
|
License: DFSG free
|
|
|
|
|
sga
??? missing short description for package sga :-(
|
| Versions of package sga |
|---|
| Release | Version | Architectures |
|---|
| trixie | 0.10.15-7 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| sid | 0.10.15-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| forky | 0.10.15-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| bullseye | 0.10.15-5 | amd64,arm64,armhf,i386 |
| bookworm | 0.10.15-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
|
License: DFSG free
|
|
|
|
|
sickle
??? missing short description for package sickle :-(
|
| Versions of package sickle |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armhf,i386 |
| bookworm | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 1.33+git20150314.f3d6ae3-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
sideretro
??? missing short description for package sideretro :-(
|
| Versions of package sideretro |
|---|
| Release | Version | Architectures |
|---|
| forky | 1.1.6-3 | amd64,arm64,armhf,i386,ppc64el,riscv64 |
| trixie | 1.1.6-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| sid | 1.1.6-3 | amd64,arm64,armhf,i386,ppc64el,riscv64 |
|
License: DFSG free
|
|
|
|
|
smalt
??? missing short description for package smalt :-(
|
| Versions of package smalt |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.7.6-13 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.7.6-13 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 0.7.6-13 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 0.7.6-9 | amd64,arm64,armhf,i386 |
| bookworm | 0.7.6-12 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
smrtanalysis
??? missing short description for package smrtanalysis :-(
|
| Versions of package smrtanalysis |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0~20210111 | all |
| bookworm | 0~20210112 | all |
| sid | 0~20210112 | all |
| trixie | 0~20210112 | all |
|
License: DFSG free
|
|
|
|
|
snap-aligner
??? missing short description for package snap-aligner :-(
|
| Versions of package snap-aligner |
|---|
| Release | Version | Architectures |
|---|
| sid | 2.0.5+dfsg-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| forky | 2.0.5+dfsg-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 2.0.3+dfsg-2 | amd64,arm64,ppc64el,riscv64 |
| bullseye | 1.0.0+dfsg-2 | amd64,arm64 |
| bookworm | 2.0.2+dfsg-1 | amd64,arm64,mips64el,ppc64el |
|
License: DFSG free
|
|
|
|
|
sniffles
??? missing short description for package sniffles :-(
|
| Versions of package sniffles |
|---|
| Release | Version | Architectures |
|---|
| forky | 2.6.0-1 | all |
| bullseye | 1.0.12b+ds-1 | amd64,arm64,armhf,i386 |
| bookworm | 2.0.7-1 | all |
| trixie | 2.6.0-1 | all |
| sid | 2.6.0-1 | all |
| upstream | 2.8.0 |
|
License: DFSG free
|
|
|
|
|
snp-sites
??? missing short description for package snp-sites :-(
|
| Versions of package snp-sites |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2.5.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 2.5.1-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 2.5.1-2 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 2.5.1-1 | amd64,arm64,armhf,i386 |
| trixie | 2.5.1-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Topics: Genetic variation
|
|
|
snpomatic
??? missing short description for package snpomatic :-(
|
| Versions of package snpomatic |
|---|
| Release | Version | Architectures |
|---|
| forky | 1.0-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 1.0-7 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.0-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1.0-5 | amd64,arm64,armhf,i386 |
| sid | 1.0-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
Please cite:
Heinrich Magnus Manske and Dominic P. Kwiatkowski:
SNP-o-matic.
(PubMed,eprint)
Bioinformatics
25(18):2434-2435
(2009)
Topics: Genetic variation; Mapping
|
|
|
soapdenovo
??? missing short description for package soapdenovo :-(
|
| Versions of package soapdenovo |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.05-6 | amd64 |
| sid | 1.05-7 | amd64 |
| forky | 1.05-7 | amd64 |
| trixie | 1.05-6 | amd64 |
| bookworm | 1.05-6 | amd64 |
|
License: DFSG free
|
Please cite:
Ruiqiang Li, Hongmei Zhu, Jue Ruan, Wubin Qian, Xiaodong Fang, Zhongbin Shi, Yingrui Li, Shengting Li, Gao Shan, Karsten Kristiansen, Songgang Li, Huanming Yang, Jian Wang and Jun Wang:
De novo assembly of human genomes with massively parallel short read sequencing.
(PubMed,eprint)
Genome Research
20(2):265-72
(2009)
|
|
|
soapdenovo2
??? missing short description for package soapdenovo2 :-(
|
| Versions of package soapdenovo2 |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 242+dfsg-3 | amd64 |
| bullseye | 242+dfsg-1 | amd64 |
| forky | 242+dfsg-5 | amd64 |
| trixie | 242+dfsg-4 | amd64 |
| sid | 242+dfsg-5 | amd64 |
|
License: DFSG free
|
Please cite:
Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang, Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu, Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian, Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam and Jun Wang:
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.
Giga Science
1(1):18
(2012)
|
|
|
sortmerna
??? missing short description for package sortmerna :-(
|
| Versions of package sortmerna |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.1-5 | amd64,i386 |
| sid | 4.3.7-3 | amd64,i386 |
| forky | 4.3.7-3 | amd64,i386 |
| trixie | 4.3.7-2 | amd64,i386 |
| bookworm | 4.3.6-2 | amd64,i386 |
| upstream | 6.0.0 |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
spades
??? missing short description for package spades :-(
|
| Versions of package spades |
|---|
| Release | Version | Architectures |
|---|
| trixie | 4.0.0+really3.15.5+dfsg-1 | amd64 |
| bullseye | 3.13.1+dfsg-2 | amd64 |
| sid | 4.0.0+really3.15.5+dfsg-3 | amd64 |
| forky | 4.0.0+really3.15.5+dfsg-3 | amd64 |
| bookworm | 3.15.5+dfsg-2 | amd64 |
| upstream | 4.2.0 |
|
License: DFSG free
|
Please cite:
Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev and Pavel A. Pevzner:
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
(PubMed,eprint)
Journal of Computational Biology
19(5):455-477
(2012)
|
|
|
sprai
??? missing short description for package sprai :-(
|
| Versions of package sprai |
|---|
| Release | Version | Architectures |
|---|
| trixie | 0.9.9.23+dfsg1-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.9.9.23+dfsg1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 0.9.9.23+dfsg1-2 | amd64,arm64,armhf,i386 |
| sid | 0.9.9.23+dfsg1-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 0.9.9.23+dfsg1-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
sra-toolkit
??? missing short description for package sra-toolkit :-(
|
| Versions of package sra-toolkit |
|---|
| Release | Version | Architectures |
|---|
| forky | 3.2.1+dfsg-6 | amd64,arm64 |
| bookworm | 3.0.3+dfsg-6~deb12u1 | amd64,arm64 |
| bullseye | 2.10.9+dfsg-2 | amd64 |
| sid | 3.2.1+dfsg-6 | amd64,arm64 |
| trixie | 3.2.1+dfsg-4 | amd64,arm64 |
| upstream | 4760-2.9.7 |
|
License: DFSG free
|
|
|
|
|
srst2
??? missing short description for package srst2 :-(
|
| Versions of package srst2 |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.2.0-8 | amd64,arm64 |
| sid | 0.2.0-14 | amd64,arm64,loong64,ppc64el,riscv64 |
| forky | 0.2.0-14 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 0.2.0-13 | amd64,arm64,ppc64el,riscv64 |
| bookworm | 0.2.0-9 | amd64,arm64,mips64el,ppc64el |
|
License: DFSG free
|
|
|
|
|
ssake
??? missing short description for package ssake :-(
|
| Versions of package ssake |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 4.0-3 | all |
| sid | 4.0.1-2 | all |
| trixie | 4.0.1-2 | all |
| forky | 4.0.1-2 | all |
| bookworm | 4.0.1-1 | all |
| Debtags of package ssake: |
|---|
| biology | nuceleic-acids |
| field | biology |
| interface | shell |
| role | program |
| scope | utility |
| use | analysing |
|
License: DFSG free
|
Topics: Sequence assembly
|
|
|
stacks
??? missing short description for package stacks :-(
|
| Versions of package stacks |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.55+dfsg-1 | amd64,arm64,armhf,i386 |
| forky | 2.68+dfsg-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 2.62+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 2.68+dfsg-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.68+dfsg-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
stringtie
??? missing short description for package stringtie :-(
|
| Versions of package stringtie |
|---|
| Release | Version | Architectures |
|---|
| forky | 3.0.3+ds-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 3.0.3+ds-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 2.2.1+ds-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 2.1.4+ds-4 | amd64,arm64,armhf,i386 |
| bookworm | 2.2.1+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
subread
??? missing short description for package subread :-(
|
| Versions of package subread |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 2.0.1+dfsg-1 | amd64,arm64,armhf,i386 |
| sid | 2.0.8+dfsg-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| bookworm | 2.0.3+dfsg-1 | amd64,arm64,armel,armhf,i386,ppc64el |
| trixie | 2.0.8+dfsg-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64 |
| forky | 2.0.8+dfsg-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64 |
| upstream | 2.1.1 |
|
License: DFSG free
|
|
|
|
|
sumaclust
??? missing short description for package sumaclust :-(
|
| Versions of package sumaclust |
|---|
| Release | Version | Architectures |
|---|
| trixie | 1.0.36+ds-4 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 1.0.36+ds-1 | amd64,arm64,armhf,i386 |
| bookworm | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| forky | 1.0.36+ds-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.0.36+ds-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
sumatra
??? missing short description for package sumatra :-(
|
| Versions of package sumatra |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.0.36+ds-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.0.36+ds-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1.0.36+ds-1 | amd64,arm64,armhf,i386 |
| forky | 1.0.36+ds-3 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
|
License: DFSG free
|
|
|
|
|
tabix
??? missing short description for package tabix :-(
|
| Versions of package tabix |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.22.1+ds2-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.22.1+ds2-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 1.11-4 | amd64,arm64,armhf,i386 |
| bookworm | 1.16+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.21+ds-1 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| upstream | 1.23.1 |
| Debtags of package tabix: |
|---|
| role | program |
| works-with-format | html |
|
License: DFSG free
|
|
|
|
|
transrate-tools
??? missing short description for package transrate-tools :-(
|
| Versions of package transrate-tools |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.0.0-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.0.0-7 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 1.0.0-3 | amd64,arm64,armhf,i386 |
| trixie | 1.0.0-5 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.0.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
|
License: DFSG free
|
|
|
|
|
trimmomatic
??? missing short description for package trimmomatic :-(
|
| Versions of package trimmomatic |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 0.39+dfsg-2 | all |
| trixie | 0.39+dfsg-2 | all |
| forky | 0.39+dfsg-2 | all |
| sid | 0.39+dfsg-2 | all |
| bookworm | 0.39+dfsg-2 | all |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
|
|
|
trinityrnaseq
??? missing short description for package trinityrnaseq :-(
|
| Versions of package trinityrnaseq |
|---|
| Release | Version | Architectures |
|---|
| sid | 2.15.2+dfsg-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 2.11.0+dfsg-6 | amd64,arm64 |
| trixie | 2.15.2+dfsg-1 | amd64,arm64,ppc64el,riscv64 |
|
License: DFSG free
|
Please cite:
Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman and Aviv Regev:
Full-length transcriptome assembly from RNA-Seq data without a reference genome..
(PubMed)
Nature Biotechnology
29(7):644-652
(2011)
|
|
|
uc-echo
??? missing short description for package uc-echo :-(
|
| Versions of package uc-echo |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.12-19 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 1.12-19 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 1.12-19 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 1.12-18 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 1.12-15 | amd64,arm64,armhf,i386 |
|
License: DFSG free
|
Topics: Data management; Sequencing
|
|
|
vcftools
??? missing short description for package vcftools :-(
|
| Versions of package vcftools |
|---|
| Release | Version | Architectures |
|---|
| sid | 0.1.17-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| trixie | 0.1.16-3 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 0.1.16-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| bullseye | 0.1.16-2 | amd64,arm64,armhf,i386 |
| forky | 0.1.17-1 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| Debtags of package vcftools: |
|---|
| role | program |
|
License: DFSG free
|
The package is enhanced by the following packages:
multiqc
Please cite:
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean and Richard Durbin:
The variant call format and VCFtools.
(PubMed,eprint)
Bioinformatics
27(15):2156-8
(2011)
|
|
|
velvet
??? missing short description for package velvet :-(
|
| Versions of package velvet |
|---|
| Release | Version | Architectures |
|---|
| bullseye | 1.2.10+dfsg1-7 | amd64,arm64,armhf,i386 |
| trixie | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.2.10+dfsg1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 1.2.10+dfsg1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| forky | 1.2.10+dfsg1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| Debtags of package velvet: |
|---|
| biology | nuceleic-acids |
| field | biology, biology:bioinformatics |
| interface | commandline |
| role | program |
| use | analysing |
|
License: DFSG free
|
|
|
|
|
velvet-long
??? missing short description for package velvet-long :-(
|
| Versions of package velvet-long |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.2.10+dfsg1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bullseye | 1.2.10+dfsg1-7 | amd64,arm64,armhf,i386 |
| trixie | 1.2.10+dfsg1-9 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bookworm | 1.2.10+dfsg1-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| forky | 1.2.10+dfsg1-10 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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velvetoptimiser
??? missing short description for package velvetoptimiser :-(
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| Versions of package velvetoptimiser |
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| Release | Version | Architectures |
|---|
| bullseye | 2.2.6-3 | all |
| sid | 2.2.6-5 | all |
| forky | 2.2.6-5 | all |
| trixie | 2.2.6-5 | all |
| bookworm | 2.2.6-5 | all |
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License: DFSG free
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vsearch
??? missing short description for package vsearch :-(
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| Versions of package vsearch |
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| Release | Version | Architectures |
|---|
| bookworm | 2.22.1-1 | amd64,arm64,ppc64el |
| trixie | 2.30.0-1 | amd64,arm64,ppc64el,riscv64 |
| sid | 2.30.4-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| forky | 2.30.4-1 | amd64,arm64,loong64,ppc64el,riscv64 |
| bullseye | 2.15.2-3 | amd64,arm64 |
| upstream | 2.31.0 |
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License: DFSG free
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wham-align
??? missing short description for package wham-align :-(
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| Versions of package wham-align |
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| Release | Version | Architectures |
|---|
| trixie | 0.1.5-8 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 0.1.5-8 | amd64,arm64,armhf,i386 |
| forky | 0.1.5-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 0.1.5-8 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| bookworm | 0.1.5-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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Please cite:
Yinan Li, Allie Terrell and Jignesh M. Patel:
WHAM: A High-throughput Sequence Alignment Method
(eprint)
Proceedings of the ACM SIGMOD International Conference on Management of Data, SIGMOD 2011, Athens, Greece
(2011)
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wigeon
??? missing short description for package wigeon :-(
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| Versions of package wigeon |
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| Release | Version | Architectures |
|---|
| forky | 20101212+dfsg1-6 | all |
| bookworm | 20101212+dfsg1-5 | all |
| trixie | 20101212+dfsg1-6 | all |
| bullseye | 20101212+dfsg1-4 | all |
| sid | 20101212+dfsg1-6 | all |
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License: DFSG free
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Please cite:
Brian J. Haas, Dirk Gevers, Ashlee M. Earl, Mike Feldgarden, Doyle V. Ward, Georgia Giannoukos, Dawn Ciulla, Diana Tabbaa, Sarah K. Highlander, Erica Sodergren, Barbara Methé, Todd Z. DeSantis, The Human Microbiome Consortium, Joseph F. Petrosino, Rob Knight and Bruce W. Birren:
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
(PubMed,eprint)
Genome Research
21(3):494-504
(2011)
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Official Debian packages with lower relevance
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nanolyse
??? missing short description for package nanolyse :-(
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| Versions of package nanolyse |
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| Release | Version | Architectures |
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| bullseye | 1.2.0-1 | amd64,arm64,armhf,i386 |
| bookworm | 1.2.0-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| trixie | 1.2.0-4 | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| forky | 1.2.0-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
| sid | 1.2.0-4 | amd64,arm64,armhf,i386,loong64,ppc64el,riscv64,s390x |
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License: DFSG free
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python3-anndata
??? missing short description for package python3-anndata :-(
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| Versions of package python3-anndata |
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| Release | Version | Architectures |
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| bookworm | 0.8.0-4 | all |
| sid | 0.12.6-1 | all |
| bullseye | 0.7.5+ds-3 | all |
| upstream | 0.12.16 |
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License: DFSG free
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r-bioc-isoformswitchanalyzer
??? missing short description for package r-bioc-isoformswitchanalyzer :-(
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| Versions of package r-bioc-isoformswitchanalyzer |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 1.20.0+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 2.6.0+ds-3 | amd64,arm64,loong64,ppc64el,riscv64 |
| trixie | 2.6.0+ds-2 | amd64,arm64,ppc64el,riscv64,s390x |
| upstream | 2.12.0 |
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License: DFSG free
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r-bioc-mofa2
??? missing short description for package r-bioc-mofa2 :-(
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| Versions of package r-bioc-mofa2 |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.16.0+ds-5 | all |
| upstream | 1.22.0 |
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License: DFSG free
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Debian packages in contrib or non-free
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cufflinks
??? missing short description for package cufflinks :-(
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| Versions of package cufflinks |
|---|
| Release | Version | Architectures |
|---|
| bookworm | 2.2.1+dfsg.1-9 (non-free) | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
| sid | 2.2.1+dfsg.1-10 (non-free) | amd64,arm64,armhf,i386,ppc64el,riscv64,s390x |
| trixie | 2.2.1+dfsg.1-10 (non-free) | amd64,arm64,armel,armhf,i386,ppc64el,riscv64,s390x |
| bullseye | 2.2.1+dfsg.1-8 (non-free) | amd64,arm64,armhf,i386 |
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License: non-free
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vdjtools
??? missing short description for package vdjtools :-(
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| Versions of package vdjtools |
|---|
| Release | Version | Architectures |
|---|
| sid | 1.2.1+git20190311+repack-2 (non-free) | all |
| forky | 1.2.1+git20190311+repack-2 (non-free) | all |
| trixie | 1.2.1+git20190311+repack-2 (non-free) | all |
| bookworm | 1.2.1+git20190311+repack-1 (non-free) | all |
| bullseye | 1.2.1+git20190311-5 (non-free) | all |
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License: non-free
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Please cite:
M Shugay, D.V. Bagaev, M.A. Turchaninova, D.A. Bolotin, O.V. Britanova, E.V. Putintseva, M.V. Pogorelyy, V.I. Nazarov VI, I.V. Zvyagin, V.I. Kirgizova, K.I. Kirgizov, E.V. Skorobogatova and D.M. Chudakov:
VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
(PubMed,eprint)
PLoS Comput Biol.
11(11):e1004503
(2015)
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Packaging has started and developers might try the packaging code in VCS
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giira
RNA-Seq driven gene finding incorporating ambiguous reads
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| Versions of package giira |
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| Release | Version | Architectures |
|---|
| VCS | 0.0.20140625-2 | all |
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License: GPL-3
Debian package not available
Version: 0.0.20140625-2
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GIIRA is a gene prediction method that identifies potential coding
regions exclusively based on the mapping of reads from an RNA-Seq
experiment. It was foremost designed for prokaryotic gene prediction
and is able to resolve genes within the expressed region of an operon.
However, it is also applicable to eukaryotes and predicts exon intron
structures as well as alternative isoforms.
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graphmap2
highly sensitive and accurate mapper for long, error-prone reads
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| Versions of package graphmap2 |
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| Release | Version | Architectures |
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| VCS | 0.6.4-1 | all |
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License: MIT
Debian package not available
Version: 0.6.4-1
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GraphMap2 is a highly sensitive and accurate mapper for long, error-
prone reads. The mapping algorithm is designed to analyse nanopore
sequencing reads, which progressively refines candidate alignments to
robustly handle potentially high-error rates and a fast graph traversal
to align long reads with speed and high precision (>95%). Evaluation on
MinION sequencing data sets against short- and long-read mappers
indicates that GraphMap increases mapping sensitivity by 10–80% and maps
95% of bases. GraphMap alignments enabled single-nucleotide variant
calling on the human genome with increased sensitivity (15%) over the
next best mapper, precise detection of structural variants from length
100 bp to 4 kbp, and species and strain-specific identification of
pathogens using MinION reads.
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mosaik-aligner
reference-guided aligner for next-generation sequencing
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| Versions of package mosaik-aligner |
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| Release | Version | Architectures |
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| VCS | 2.2.30+20140627-1 | all |
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License: MIT
Debian package not available
Version: 2.2.30+20140627-1
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MosaikBuild converts various sequence formats into Mosaik’s native read
format. MosaikAligner pairwise aligns each read to a specified series of
reference sequences. MosaikSort resolves paired-end reads and sorts the
alignments by the reference sequence coordinates. Finally, MosaikText
converts alignments to different text-based formats.
At this time, the workflow consists of supplying sequences in FASTA,
FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
the Illumina ELAND formats.
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nanoplot
plotting scripts for long read sequencing data
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| Versions of package nanoplot |
|---|
| Release | Version | Architectures |
|---|
| VCS | 1.36.2-1 | all |
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License: MIT
Debian package not available
Version: 1.36.2-1
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NanoPlot provides plotting scripts for long read sequencing data.
These scripts perform data extraction from Oxford Nanopore sequencing data
in the following formats:
- fastq files (optionally compressed)
- fastq files generated by albacore, guppy or MinKNOW containing additional
information (optionally compressed)
- sorted bam files
- sequencing_summary.txt output table generated by albacore, guppy or
MinKnow basecalling (optionally compressed)
- fasta files (optionally compressed)
- multiple files of the same type can be offered simultaneously
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umap
quantify genome and methylome mappability
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| Versions of package umap |
|---|
| Release | Version | Architectures |
|---|
| VCS | 1.0.0-1 | all |
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License: GPL-3.0
Debian package not available
Version: 1.0.0-1
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Umap identifies uniquely mappable regions of any genome. Its Bismap
extension identifies mappability of the bisulfite converted
genome (methylome).
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No known packages available
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annovar
annotate genetic variants detected from diverse genomes
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License: Open Source for non-profit
Debian package not available
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ANNOVAR is an efficient software tool to utilize update-to-date information
to functionally annotate genetic variants detected from diverse genomes
(including human genome hg18, hg19, as well as mouse, worm, fly, yeast and
many others). Given a list of variants with chromosome, start position, end
position, reference nucleotide and observed nucleotides, ANNOVAR can perform:
1. Gene-based annotation: identify whether SNPs or CNVs cause protein coding
changes and the amino acids that are affected. Users can flexibly use RefSeq
genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition
systems.
2. Region-based annotations: identify variants in specific genomic regions,
for example, conserved regions among 44 species, predicted transcription
factor binding sites, segmental duplication regions, GWAS hits, database
of genomic variants, DNAse I hypersensitivity sites, ENCODE
H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many
other annotations on genomic intervals.
3. Filter-based annotation: identify variants that are reported in dbSNP,
or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project,
or identify subset of non-synonymous SNPs with SIFT score>0.05, or many
other annotations on specific mutations.
4. Other functionalities: Retrieve the nucleotide sequence in any
user-specific genomic positions in batch, identify a candidate gene list
for Mendelian diseases from exome data, identify a list of SNPs from
1000 Genomes that are in strong LD with a GWAS hit, and many other
creative utilities.
In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for
4.7 million variants, ANNOVAR requires ~4 minutes to perform
gene-based functional annotation, or ~15 minutes to perform stepwise
"variants reduction" procedure, making it practical to handle hundreds
of human genomes in a day.
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forge
genome assembler for mixed read types
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License: Apache 2.0
Debian package not available
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Forge Genome Assembler is a parallel, MPI based genome assembler for
mixed read types.
Forge is a classic "Overlap layout consensus" genome assembler written
by Darren Platt and Dirk Evers. Implemented in C++ and using the
parallel MPI library, it runs on one or more machines in a network and
can scale to very large numbers of reads provided there is enough
collective memory on the machines used. It generates a full consensus
alignment of all reads, can handle mixtures of sanger, 454 and illumina
reads. There is some support for solid color space and it includes built
in tools for vector trimming and contamination screening.
Forge and was originally developed at Exelixis and they have kindly
agreed to place the software which underwent much subsequent development
outside Exelixis, into the public domain. Forge works with most of the
common MPI implementations.
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