Debian Med Project
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Summary
Next generation sequencing
Debian Med bioinformatics applications usable in Next Generation Sequencing

It aims at gettting packages which specializes in alignment of sequences produced by next generation sequencing.

The list to the right includes various software projects which are of some interest to the Debian Med Project. Currently, only a few of them are available as Debian packages. It is our goal, however, to include all software in Debian Med which can sensibly add to a high quality Debian Pure Blend.

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

Debian Med Next generation sequencing packages

Official Debian packages with high relevance

Bedtools
Programpakke med redskaber for sammenligning af arvemassefunktioner
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BEDTools-redskaber giver mulighed for at adressere gængse arvemasseopgaver såsom at finde funktionsoverlap og beregne dækning. Redskaberne er hovedsagelig baseret på fire meget udbredte filformater: BED, GFF/GTF, VCF og SAM/BAM. Med brug af BEDTools kan du udvikle sofistikerede datakanaler, som besvarer komplicerede forskningsspørgsmål ved at udsende flere BEDTools sammen.

Redskabet groupBy er distribueret i pakken filo.

Please cite: Aaron R. Quinlan and Ira M. Hall: BEDTools: a flexible suite of utilities for comparing genomic features. (PubMed,eprint) Bioinformatics 26(6):841-842 (2010)
Bowtie
Ultrahurtig og hukommelseseffektiv short read-sammenligner
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Denne pakke adresserer problemet med at fortolke resultaterne fra de seneste (2010) DNA-sekvensteknologier. Disse vil resultere i ret så korte stræk og disse kan ikke fortolkes direkte. Det er udfordringen for værktøjer såsom Bowtie at give en kromosonplacering til korte stræk af DNA sekventeret per kørsel.

Bowtie sammenligner korte DNA-sekvenser (læsninger) for den menneskelige arvemasse med en hastighed på mere end 25 millioner 35-bp læsninger per time. Bowtie indekserer arvemassen med et Burrows-Wheeler-indeks for at holde hukommelsesaftrykket lavt: Typisk omkring 2,2 GB for den menneskelige arvemasse (2,9 GB for paired-end).

The package is enhanced by the following packages: bowtie-examples
Please cite: Ben Langmead, Cole Trapnell, Mihai Pop and Steven L Salzberg: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. (eprint) Genome Biology 10:R25 (2009)
Bwa
Burrows-Wheeler Aligner (sekvenssammenligner)
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Burrows-Wheeler Aligner (BWA) er en programpakke, for oversættelse af lavafvigende sekvenser mod en stor referencearvemasse, såsom den menneskelige arvemasse. Den består af tre algoritmer: BWA-backtrack, BWA-SW og BWA-MEM. Den første algoritme er designet for Illunina-sekvenslæsninger op til 100 bp, mens de sidste to er for længere sekvenser fra 70 bp til 1 Mbp. BWA-MEM og BWA-SW deler funktioner såsom understøttelse af long-read og opdelingssammenligning, men BWA-MEM, som er den seneste, anbefales generelt for højkvalitets forespørgsler, da den er hurtigere og mere præcis. BWA-MEM har også bedre ydelse end BWA-backtrack for 70-100 bp Illumina-læsninger.

Please cite: Heng Li and Richard Durbin: Fast and accurate short read alignment with Burrows-Wheeler transform. (PubMed,eprint) Bioinformatics 25(14):1754-1760 (2009)
Fastx-toolkit
forbehandlingsværktøjer til læsning af korte FASTQ/A-nukleotider
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FASTX-Toolkit er en samling af kommandolinjeværktøjer for forbehandling af korte nukleotidlæsninger i FASTA- og FASTQ-formater, normalt udarbejdet af Next-Generation sekvensmaskiner. Hovedbehandlingen af sådanne FASTA/FASTQ-filer er oversættelse (justering) af sekvenserne til referencegenomer eller andre databaser der bruger specialiserede programmer såsom BWA, Bowtie og mange andre. Det er dog undertiden mere produktivt at forbehandle FASTA/FASTQ-filerne, forud for oversættelse af sekvenserne til genom-manipulering, for at fremstille bedre oversættelsesresultater. FASTX-Toolkit-værktøjer udfører nogle af disse forbehandlingsopgaver.

Filo
FILe and stream Operations
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The following tools are available as part of the filo package:

groupBy – mimics the “groupBy” clause in database systems.

shuffle – randomize the order of lines in a file.

stats – computes descriptive statistic on a given column of a tab-delimited file or stream.

Because their name is too generic, ‘shuffle’ and ‘stats’ are relocated in /usr/lib/filo.

Kissplice
Detection of various kinds of polymorphisms in RNA-seq data
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KisSplice is a piece of software that enables the analysis of RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows one to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

Please cite: Gustavo AT Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo and Vincent Lacroix: KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. (PubMed,eprint) BMC Bioinformatics 13((Suppl 6)):S5 (2012)
Last-align
sammenligning af biologisk sekvenser på genom-skala
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LAST er programmel til sammenligning og justering af sekvenser, typisk DNA- eller protein-sekvenser. LAST ligner BLAST, men det er bedre til at håndtere meget store mængder af sekvensdata. Her er to ting som LAST er god til:

  • Sammenligning af store (eksempelvis pattedyrs) genomer.
  • Kortlægge masser af sekvens-mærker oven på et genom.

Den primære, tekniske innovation er at LAST finder indledende samstemmende forekomster, baseret på deres mangfoldighed, i stedet for at benytte en fast størrelse (BLAST bruger eksempelvis 10-mers). Dette gør, at man kan kortlægge mærker til genomer, uden gentagelsesmaskering (eng. »repeat- masking«), uden at blive overvældet af gentagne forekomster. For at finde disse forekomster som har forskellige størrelser, så bruger den en suffiks- række (inspireret af Vmatch). For at opnå høj følsomhed, så bruger den en usammenhængende suffiks-række, der er en analog til frø som placeres med mellemrum.

Please cite: Martin C. Frith, Raymond Wan and Paul Horton: Incorporating sequence quality data into alignment improves DNA read mapping. (PubMed,eprint) Nucl. Acids Res. 38(7):e100 (2010)
Maq
kortlægger korte, fast-længde, polymorfiske DNA-sekvenslæsninger til reference-sekvenser
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Maq (forkortelse af »Mapping and Assembly with Quality«) bygger kortlagte montager fra korte læsninger genereret af næste generation inden for maskiner til sekvensering. Det blev særligt designet til »Illumina-Solexa 1G Genetic Analyzer«, og har indledende funktionalitet til at håndtere ABI SOLid-data. Maq var tidligere kendt som mapass2.

Udvikling af Maq stoppede i 2008. Dets efterfølger er BWA og SAMtools.

Please cite: Heng Li, Jue Ruan and Richard Durbin: Mapping short DNA sequencing reads and calling variants using mapping quality scores. (PubMed,eprint) Genome Research 18(11):1851-1858 (2008)
Mira-assembler
Hel Genome Shotgun og EST Sequence Assembler
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Mira er en specialiseret gensekvenssamler for sekvensprojekter regnet som »svære« på grund af et stort antal ensformige gentagelser. For expressed sequence tags-transskriptioner (EST'er) er miraEST specialiseret på rekonstruktion af urørte mRNA-transskriptioner mens det detekterer og klassificerer enlige nukleotidpolymorfismer (SNP), der opstår i forskellige variationer herudfra.

Sekvenssamleren bruges rutinemæssigt til forskellige opgaver såsom mutationsdetektering i forskellige celletyper, analyser af ligheder i transskriptioner mellem organismer og samling af urørte sekvenser fra forskellige kilder for oligodesign i kliniske mikroarrayeksperimenter.

Pakken tilbyder følgende kørbare filer:

  • mira: for samling af genomsekvenser
  • miramem: estimerer hukommelsen krævet af et projekt. Fungerer ved at lænke til mira.
  • convert_project: til konvertering af projektfiltyper til andre typer
  • caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf og gbf2fasta er nogle ofte anvendte filkonverteringsprogrammer (fungerer ved at lænke til convert_project)
  • scftool: Værktøjssæt som er nyttigt når der arbejdes med SCF-sporfiler
  • fastatool: Værktøjssæt som er nyttigt når der arbejdes med FASTA- sporfiler

  • fasta2frag: fragmentering af sekvenser til mindre, overlappende sekvenser. Nyttig til simulering af haglgeværsekvenser. Kan oprette undersekvenser i begge retninger (/default) og også parrede slutsekvenser.

  • fastaselect: givet en FASTA-fil (og eventuelt en FASTA- kvalitetsfil) og en fil med navne til læsning, vælges sekvenserne fra FASTA (og kvalitetsfil) og skrives til en resulterende FASTA
  • fastqselect: ligesom fastaselect.tcl, men til FASTQ
  • fixACE4consed: Consed indeholder en fejl som gør det umuligt for den at læse konsensusmærker i ACE-filer skrevet af MIRA-samleren (og muligvis andre programmer). Dette skript behandler en ACE-fil sådan at consed kan læse konsensusmærkerne.
Please cite: Bastien Chevreux, Thomas Pfisterer, Bernd Drescher, Albert J. Driesel, Werner E. G. Müller, Thomas Wetter and Sándor Suhai: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. (PubMed,eprint) Genome Research 14(6):1147-1159 (2004)
Mothur
Programpakke for sekvensanalyse til forskning i mikrobiota
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Mothur søger at udvikle et enkelt stykke open source program, der kan udvides til at fylde bioinformatikbehov i mikrobiel økologisamfund. Den har indbygget funktionalitet for dotur, sons, treeclimber, s-libshuff, unifrac og meget mere. Ud over at forbedre fleksibiliteten af disse algoritmer er en række andre funktioner, herunder regnemaskiner og visualiseringsværktøjer, blevet tilføjet.

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)
Picard-tools
Command line tools to manipulate SAM and BAM files
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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Picard Tools includes these utilities to manipulate SAM and BAM files: BamToBfq IlluminaBasecallsToSam BuildBamIndex MarkDuplicates CalculateHsMetrics MeanQualityByCycle CleanSam MergeBamAlignment CollectAlignmentSummaryMetrics MergeSamFiles CollectGcBiasMetrics NormalizeFasta CollectInsertSizeMetrics QualityScoreDistribution CollectRnaSeqMetrics ReplaceSamHeader CompareSAMs RevertSam CreateSequenceDictionary SamFormatConverter ExtractIlluminaBarcodes SamToFastq EstimateLibraryComplexity SortSam FastqToSam ValidateSamFile FixMateInformation ViewSam

Qiime
Quantitative Insights Into Microbial Ecology
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QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including

  • Sanger,
  • Roche/454, and
  • Illumina GAIIx. With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform

  • library de-multiplexing and quality filtering;

  • denoising with PyroNoise;
  • OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools;
  • taxonomy assignment with BLAST or the RDP classifier;
  • sequence alignment with PyNAST, muscle, infernal, or other tools;
  • phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;
  • alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species;
  • beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis;
  • summarization and visualization of taxonomic composition of samples using pie charts and histograms and many other features.

QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses.

Please cite: J Gregory Caporaso, Justin Kuczynski, Stombaugh Jesse, Bittinger Kyle, Bushman Frederic D, Costello Elizabeth K, Fierer Noah, Pena Antonio Gonzalez, Goodrich Julia K, Gordon Jeffrey I, Huttley Gavin A, Kelley Scott T, Knights Dan, Koenig Jeremy E, Ley Ruth E, Lozupone Catherine A, McDonald Daniel, Muegge Brian D, Pirrung Meg, Reeder Jens, Sevinsky Joel R, Turnbaugh Peter J, Walters William A, Widmann Jeremy, Yatsunenko Tanya, Zaneveld Jesse and Knight Rob: QIIME allows analysis of high-throughput community sequencing data. (PubMed) Nature Methods 7:335 - 336 (2010)
R-bioc-edger
Empirisk analyse af digitale gen-udtryksdata i R
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Biokonduktor-pakke til differentieret udtryksanalyse af hel transkriptom- sekventering (RNA-seq) og digitale gen-udtryksprofiler med biologisk replikation. Det bruger empirisk Bayes-estimering og præcise test baseret på den negative binomial-fordelingsdistribution. Det er også nyttigt for differentieret signal-analyse med andre typer optællinger af genom-skala.

Please cite: Mark D. Robinson and Gordon K. Smyth: Moderated statistical tests for assessing differences in tag abundance. (PubMed,eprint) Bioinformatics 23(21):2881-2887 (2007)
R-bioc-hilbertvis
GNU R-pakke til at visualisere lange vektordata
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Dette værktøj giver dig mulighed for at vise meget lange datavektorer på en pladseffektiv måde, ved at organisere dataene via en 2D-Hilbertkurve. Brugeren kan så visuelt bedømme den store skalastruktur og distribution af funktioner på samme tid via den rå form og intensiteten for individuelle funktioner.

I bioinformatics er et typisk brugstilfælde ChIP-Chip og ChIP-Seq, eller grundlæggende alle slags genomdata, som passende vises som kvantitative spor (»wiggle data«) i genombrowsere såsom dem tilbudt af Ensembl eller UCSC.

Please cite: Simon Anders: Visualization of genomic data with the Hilbert curve. (PubMed,eprint) Bioinformatics 25(10):1231-1235 (2009)
Samtools
Forarbejdning af sekvensopstillinger i SAM- og BAM-formater
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Samtools er et sæt af værktøjer, der manipulerer nukleotidsekvensjusteringer i det binære BAM-format. Værkøjet importerer fra og eksporterer til ascii SAM-formatet (sekvensjustering/map), udfører sortering, sammenlægning og indeksering, og gør det muligt at hente læsninger i alle områder hurtigt. Det er designet til at arbejde på en strøm, og er i stand til at åbne en BAM-fil (ikke SAM) på en ekstern FTP- eller HTTP-server.

The package is enhanced by the following packages: libbio-samtools-perl
Please cite: Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map (SAM) Format and SAMtools. (PubMed,eprint) Bioinformatics 25(16):2078-2079 (2009)
Sra-toolkit
utilities for the NCBI Sequence Read Archive
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Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq.

The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE.

The "help" information will be improved in near future releases, and the tool options will become standardized across the set. More documentation will also be provided documentation on the NCBI web site.

Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts.

Please cite: Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino and Guy Cochrane: Improvements to services at the European Nucleotide Archive. (PubMed,eprint) Nucleic Acids Research 38(Database issue):D39-45 (2010)
Ssake
Genomprogram for samling af millioner af meget korte DNA-sekvenser
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Short Sequence Assembly af K-mer search and 3′ read Extension (SSAKE) er et genomprogram for aggressiv samling af millioner af korte nukleotidsekvenser ved gradvis at søge efter perfekte 3'-meste k-merer ved hjælp af et DNA-præfikstræ. SSAKE er designet til at hjælpe med at udnytte oplysningerne fra korte sekvenser læst ved stringent klyngeopbygning i contig'er, der kan bruges til at karakterisere nye sekventeringsmål.

Please cite: Rene L. Warren, Granger G. Sutton, Steven J. M. Jones and Robert A. Holt: Assembling millions of short DNA sequences using SSAKE. (PubMed,eprint) Bioinformatics 23(4):500-501 (2007)
Tabix
Generisk indeksprogram for TAB-afgrænsede arvemassepositionsfiler
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Tabix indekserer filer hvor nogle kolonner indikerer sekvenskoordinater: navn (normalt et kromosom), start og stop. Inddatafilen skal være positionssorteret og komprimeret af bgzip (tilbudt i denne pakke), som har en grænseflade der ligner gzip. Efter indeksering er tabix i stand til hurtigt at hente datalinjer efter kromosomkoordinater. Hurtig dataindhentelse fungerer også over netværk hvis en URI angives som et filnavn.

Please cite: Li, Heng: Tabix: Fast retrieval of sequence features from generic TAB-delimited files. (PubMed,eprint) Bioinformatics 27(5):718-9 (2011)
Tophat
fast splice junction mapper for RNA-Seq reads
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TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.

The package is enhanced by the following packages: cufflinks
Please cite: Cole Trapnell, Lior Pachter and Steven L. Salzberg: TopHat: discovering splice junctions with RNA-Seq. (PubMed,eprint) Bioinformatics 25(9):1105-1111 (2009)
Uc-echo
error correction algorithm designed for short-reads from NGS
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ECHO is an error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina's Genome Analyzer II. The algorithm uses a Bayesian framework to improve the quality of the reads in a given data set by employing maximum a posteriori estimation.

Vcftools
Collection of tools to work with VCF files
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VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.

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
Sekvens-assembler for nukleinsyre til meget korte læsninger
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Velvet er en »de novo«-genomisk assembler som er specielt designet for teknologier til kort læsning, såsom Solexa eller 454, udviklet af Daniel Zerbino og Ewan Birney ved European Bioinformatics Institue (EMBL-EBI), nær Cambridge, i Storbritannien.

Velvet kan i øjeblikket tage korte læsesekvenser, fjerner fejl og fremstiller dernæst unikke »contig'er« i høj kvalitet. Det anvender derefter parvis læseinformation, hvis tilgængelig, til at indhente de gentagne områder mellem contig'erne.

Please cite: Daniel R. Zerbino and Ewan Birney: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. (PubMed,eprint) Genome Research 18(5):821-829 (2008)

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Cufflinks
Transcript assembly, differential expression and regulation for RNA-Seq
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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.

Please cite: Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold and Lior Pachter: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (PubMed) Nature Biotechnology 28(5):511-515 (2010)

Packaging has started and developers might try the packaging code in VCS

Mosaik-aligner
reference-guided aligner for next-generation sequencing
License: MIT
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Version: 1.1.0021-1

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.

No known packages available

Annovar
annotate genetic variants detected from diverse genomes
License: Open Source for non-profit
Debian package not available

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.

Forge
genome assembler for mixed read types
License: Apache 2.0
Debian package not available

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.

Remark of Debian Med team: Competitor to MIRA2 and wgs-assembler

This package was requested by William Spooner whs@eaglegenomics.com as a competitor to MIRA2 and wgs-assembler.

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