Bowtie

An ultrafast memory-efficient short read aligner

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Pre-built indexes

Consider using Illumina's iGenomes collection. Each iGenomes archive contains pre-built Bowtie and Bowtie 2 indexes.

H. sapiens, UCSC hg18 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, UCSC hg19 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, NCBI v36 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
H. sapiens, NCBI v37 2.7 GB
 or: part 1 - 1.7 GB, part 2 - 1.0 GB
 colorspace: full, or part 1, part 2
M. musculus, UCSC mm8 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
M. musculus, UCSC mm9 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
M. musculus, NCBI v37 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
R. norvegicus, UCSC rn4 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
B. taurus, UMD v3.0 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
C. familiaris, UCSC canFam2 2.4 GB
 or: part 1 - 1.5 GB, part 2 - 900 MB
 colorspace: full, or part 1, part 2
G. gallus, UCSC, galGal3 1.1 GB
 colorspace: full
D. melanogaster, Flybase, r5.22 150 MB
 colorspace: full
A. thaliana, TAIR, TAIR9 120 MB
 colorspace: full
C. elegans, Wormbase, WS200 75 MB
 colorspace: full
S. cerevisiae, CYGD 15 MB
 colorspace: full
E. coli, NCBI, st. 536 5 MB
 colorspace: full

All indexes 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.

Publications

Other Documentation

Authors

Links

Tools that use Bowtie (or Bowtie 2):

OS distributions with Bowtie packages

Commercial products using Bowtie:

Published protocols using Bowtie 1 and/or 2: