Bowtie - Manual

Bowtie An ultrafast memory-efficient short read aligner Site Map Home News archive Getting started Manual Latest Release Bowtie 0.12.79/7/10 Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. For release updates, subscribe to the mailing list. Related Tools Crossbow: Genotyping, cloud computing Tophat: RNA-Seq splice junction mapper Cufflinks: Iso assembly, quantitation Myrna: Cloud, differential gene expression Pre-built inds H. sapiens, UCSC hg182.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, UCSC hg192.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, NCBI v362.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 H. sapiens, NCBI v372.7 GB or: part 1 - 1.7 GB, part 2 - 1.0 GB colorspace: full, or part 1, part 2 M. musculus, UCSC mm82.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 M. musculus, UCSC mm92.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 M. musculus, NCBI v372.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 Bowtie: Manualhttp://bowtie- 1 of 2014.07.2011 10:56 R. norvegicus, UCSC rn42.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 B. taurus, UMD v3.02.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 C. familiaris, UCSC canFam22.4 GB or: part 1 - 1.5 GB, part 2 - 900 MB colorspace: full, or part 1, part 2 G. gallus, UCSC, galGal31018 MB colorspace: full D. melanogaster, Flybase, r5.22150 MB colorspace: full A. thaliana, TAIR, TAIR9120 MB colorspace: full C. elegans, Wormbase, WS20075 MB colorspace: full S. cerevisiae, CYGD15 MB colorspace: full E. coli, NCBI, st. 5365 MB colorspace: full All inds are for assemblies, not contigs. Unplaced or unlocalized sequences and alternate haplotype assemblies are excluded. Some unzip programs cannot handle archives 2 GB. If you have problems downloading or unzipping a 2 GB index, try downloading in two parts. Check .zip file integrity with MD5s. Pre-built inds are compatible with Bowtie versions 0.9.8 and later. For older inds, please contact us. Publications Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10:R134. Trapnell C, Pachter L, Salzberg SL, TopHat: discovering splice junctions with RNA-Seq. Bioinatics 2009 25(9):1105-1111. Other Documentation AGBT poster, 2/09 (.ppt, .pdf) NCBI Presentation, 11/08 (.ppt, .pdf) UMD Biosciences poster, 11/08 (.ppt, .pdf) Authors Ben Langmead Cole Trapnell Links Bowtie project Bowtie: Manualhttp://bowtie- 2 of 2014.07.2011 10:56 Request a feature Report a bug Mail