| description | de novo, parallel, paired-end sequence assembler that is designed for short reads |
| version | 1.2.6 |
| homepage | http://www.bcgsc.ca/platform/bioinfo/software/abyss |
| commands | abyss-tofastq abyss-adjtodot ABYSS abyss-fac abyss-pe abyss-joindist abyss2ace abyss2afg AdjList DistanceEst KAligner MergePaths MergeContigs PathConsensus Overlap abyss-fixmate ParseAligns PopBubbles SimpleGraph Consensus PathOverlap |
| manpages | ABYSS |
| documentation | |
| interfaces |
| description | AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. |
| version | 2.0.8 |
| homepage | http://sourceforge.net/apps/mediawiki/amos/ |
| commands | hawkeye bank-transact message-extract message-validate message-count bank2contig bank2coverage bank2fasta bank2scaff bank-clean bank-combine bank-mapping bank-report bank-tutorial dumpFeatures dumpmates extractContig dumpreads findMissingMates grow-readbank listReadPlacedStatus listGCContent load-overlaps loadFeatures normalizeScaffold renameReads resetFragLibrary revScaffold select-reads updateBankPositions updateClrRanges dumpContigsAsReads updateLibSizes bank-unlock.pl arrive arrive2 count-kmers frg-umd-merge gap-link hash-overlap kmer-count kmer-cov make-consensus make-consensus_poly merge-contigs missing-reads ovl-degr-dist po-align readinfo2cam running-cmp show-ma-asm sim-cover-depth sim-cover2 sim-shotgun verify-layout tigger contig-cmp excl_seqs.pl findChimeras.pl find_ends.pl fixfrg.pl iterate.pl kmers.pl singles.pl tab2ovls.pl trimends.pl trimfrg.pl vecfix.pl Bundler clk casm-layout casm-breaks casm-libsize pyrosim tandemCollapse trace_comment trace_comments trace_convert trace_seq trace_scf_dump fattenContig insertGapColumn manageContigs revContig rotateContig stitchContigs trimContig zipContigs zipalign.pl autoJoiner.pl asmQC2 asmQC astats analyze-read-depth cestat-cov insert-sizes listSingletonMates library-histogram list-linked-contigs scaffoldRange2Ungapped coords2cam.pl fixlib.pl postCAqc.pl tiling2cam.pl findTcovSnp.pl clusterSnps.pl listSurrogates.pl suspiciousfeat2region.pl find-query-breaks.pl barcode-graph build-persistent-bank auto-fix-contigs persistent-read-dist persistent-fix-contigs read-evolution gap-closure-reads mate-evolution listcontigreads.sh trimByOvl runAmos analyzeSNPs recallConsensus cvgStat benchmark_qual.pl benchmark_seq.pl ctgovl.pl filter_contig.pl filterfrg.pl cvgChop.pl getN50.pl getlengths.pl preTA.pl pullTArchive.pl runTA.pl preassembleFrgs.pl ktrimfrg.pl translate-fasta.pl delta2cvg.pl delta2clr.pl updateDeltaClr.pl nucmerAnnotate.pl nucmer2ovl.pl sort2.pl ovl2OVL.pl ace2contig.pl amos2frg.pl amos2mates.pl amos2sq.pl amos2ace.pl arachne2ctg.pl arachne2scaff.pl benchmark2arachne.pl benchmark2ca.pl benchmark2mates.pl benchmark2ta.pl ca2ctg.pl ca2mates.pl ca2scaff.pl ca2ta.pl cgb2ctg.pl contig2contig.pl ctg2fasta.pl ctg2umdcontig.pl frg2fasta.pl frg2ta.pl ta2ace.pl tarchive2amos.pl tarchive2ca.pl toAmos.pl toArachne.pl scaff2fasta.pl parsecasm.pl castats.pl ca2singletons.pl phd2afg.pl zipContigs |
| manpages | |
| documentation | |
| interfaces |
| description | Bowtie is an ultrafast, memory-efficient short read aligner. |
| version | 0.12.7 |
| homepage | http://bowtie-bio.sourceforge.net |
| commands | bowtie-build bowtie bowtie-inspect |
| manpages | |
| documentation | |
| interfaces |
| description | Burrows-Wheeler Aligner BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. |
| version | 0.5.9 |
| homepage | http://bio-bwa.sourceforge.net |
| commands | bwa solid2fastq qualfa2fq sracsfq2fq |
| manpages | bwa |
| documentation |
http://bioweb2.pasteur.fr/docs/bwa/bwa.html |
| interfaces |
| description | DNA sequence assembly program. |
| version | |
| homepage | http://seq.cs.iastate.edu/ |
| commands | cap3 formcon |
| manpages | cap3 |
| documentation | |
| interfaces | cap3 |
| description | Consed is a tool for viewing, editing, sequence assemblies created with phrap. |
| version | 19 |
| homepage | http://bozeman.mbt.washington.edu/consed/consed.html |
| commands | consed mktrace phd2fasta phredPhrap polyphredPhrap prp sff2scf transferConsensusTags.perl testSocket.perl tagRepeats.perl selectRegions.perl ace2Fasta.perl ace2Oligos.perl add454Reads.perl addReads2Consed.perl addSolexaReads.perl alignSolexaReads2Refs.perl amplifyTranscripts.perl countEditedBases.perl determineReadTypes.perl fasta2Ace.perl fasta2Phd.perl filter454Reads.perl phd2Ace.perl findSequenceMatchesForConsed.perl lib2Phd.perl makePhdBall.perl orderPrimerPairs.perl revertToUneditedRead removeReads |
| manpages | |
| documentation | |
| interfaces |
| description | EagleView is an information-rich genome assembler viewer with data integration capability. |
| version | 1.83 |
| homepage | http://bioinformatics.bc.edu/marthlab/EagleView |
| commands | eagleview EagleIndexFasta EagleIndexSff EagleIndexSffM |
| manpages | |
| documentation | |
| interfaces |
| description | ClustalW is a general purpose multiple alignment program for DNA or proteins. |
| version | 1.2.2 |
| homepage | |
| commands | gap5 tg_index |
| manpages | |
| documentation | |
| interfaces |
| description | GigaBayes is a short-read SNP and short-INDEL discovery program. |
| version | beta |
| homepage | http://bioinformatics.bc.edu/marthlab/GigaBayes |
| commands | PyroBayes pbShort ace2Baa baa2Ace bas2Fasta fasta2Bas |
| manpages | |
| documentation | |
| interfaces |
| description | Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. |
| version | 0.7.1 |
| homepage | http://maq.sourceforge.net |
| commands | maq maq.pl maq_eval.pl fq_all2std.pl |
| manpages | |
| documentation | |
| interfaces |
| description | Maqview is graphical read alignment viewer |
| version | 0.2.5 |
| homepage | http://maq.sourceforge.net |
| commands | maqview maqindex maqindex_socks zrio |
| manpages | |
| documentation | |
| interfaces |
| description | Identification of transcription factor binding sites in ChIP-Seq data |
| version | 1.0 |
| homepage | http://bioinfo-out.curie.fr/projects/micsa/ |
| commands | micsa FindPeaks DeleteRegions Summary FilterPeaks |
| manpages | |
| documentation | |
| interfaces |
| description | MOSAIK is a suite comprising of three modular programs: MosaikBuild, MosaikAligner, and MosaikAssembler. |
| version | beta2007 |
| homepage | http://bioinformatics.bc.edu/marthlab/Mosaik |
| commands | MosaikAligner MosaikAssembler MosaikBuild |
| manpages | |
| documentation | |
| interfaces |
| description | PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. |
| version | 5.04 |
| homepage | http://droog.mbt.washington.edu/PolyPhred.html |
| commands | polygen polyphred sudophred |
| manpages | polyphred |
| documentation |
http://bioweb2.pasteur.fr/docs/polyphred/ |
| interfaces |
| description | VAAL is a polymorphism discovery algorithm for short reads |
| version | 1.6 |
| homepage | http://www.broadinstitute.org/science/software/ |
| commands | VAAL1_5 VAAL0_5 VAAL1 VAAL0 VAAL3 VAAL2 VAAL4 ImperfectLookupTable ShortQueryLookup ScaffoldAccuracy QueryLookupTable TruePoly MakeLookupTable VAAL VAALCompareCompound VAALrun Qualb Fastb |
| manpages | VAAL_manual.pdf |
| documentation |
http://bioweb2.pasteur.fr/docs/VAAL/VAAL_manual.pdf |
| interfaces |
| description | Sequence assembler for very short reads |
| version | 1.1.02 |
| homepage | http://www.ebi.ac.uk/~zerbino/velvet/ |
| commands | velveth velvetg shuffleSequences_fasta.pl shuffleSequences_fastq.pl enlarge_exons.pl gff2fasta.pl merge_gtf_exons.pl |
| manpages | |
| documentation |
http://bioweb2.pasteur.fr/docs/velvet/Manual.pdf http://bioweb2.pasteur.fr/docs/velvet/Columbus_manual.pdf |
| interfaces |
| description | Sequence assembler for very short reads |
| version | v 4 |
| homepage | http://hgdownload.cse.ucsc.edu/downloads.html |
| commands | wigToBigWig |
| manpages | |
| documentation | |
| interfaces |