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 10R25. 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 1056 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 10R25. Langmead B, Schatz M, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology 10R134. Trapnell C, Pachter L, Salzberg SL, TopHat discovering splice junctions with RNA-Seq. Bioinatics 2009 2591105-1111. 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 1056 Request a feature Report a bug Mail