Bowtie

An ultrafast memory-efficient short read aligner

Site Map

Latest Release

Links

Related Tools

Pre-built indexes

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

H. sapiens, NCBI GRCh38 2.7 GB
H. sapiens, NCBI GRCh38
with 1KGenomes major SNPs
2.7 GB
  How we built this, FASTA
H. sapiens, UCSC hg19 2.7 GB
 colorspace: full
H. sapiens, UCSC hg19
with 1KGenomes major SNPs
2.7 GB
  How we built this, FASTA
H. sapiens, UCSC hg18 2.7 GB
 colorspace: full
H. sapiens, NCBI v37 2.7 GB
 colorspace: full
H. sapiens, NCBI v36 2.7 GB
 colorspace: full
M. musculus, UCSC mm8 2.4 GB
 colorspace: full
M. musculus, UCSC mm9 2.4 GB
 colorspace: full
M. musculus, NCBI v37 2.4 GB
 colorspace: full
R. norvegicus, UCSC rn4 2.4 GB
 colorspace: full
B. taurus, UMD v3.0 2.4 GB
 colorspace: full
C. familiaris, UCSC canFam2 2.4 GB
 colorspace: full
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

Contributors

Related links

hg18.ebwt.zip: H. sapiens, UCSC hg18   2.7 GB
MD5: 8a313f12579e0fffaf2126d997b94048
hg18.ebwt.1.zip: Part 1   1.7 GB
MD5: 93baa2b0272f7378f7ff3b68e7a5f157
hg18.ebwt.2.zip: Part 2   1.0 GB
MD5: 3a2b71dd7d6da9d7a261437391c2ea94
hg19.ebwt.zip: H. sapiens, UCSC hg19   2.7 GB
MD5: 388cb76f35d7e39ab3696623a21b78d5
hg19.ebwt.1.zip: Part 1   1.7 GB
MD5: 2a1349072ce21d200421dd12d59aa491
hg19.ebwt.2.zip: Part 2   1.0 GB
MD5: 7169cbf5108b1734e0c4e6d0e3931255
h_sapiens_asm.ebwt.zip: H. sapiens, NCBI 36.3   2.7 GB
MD5: 1003dd89d77f086c80c8b0b723ecf68b
h_sapiens_asm.ebwt.1.zip: Part 1   1.7 GB
MD5: b97a9f2640a86ee21175617de6080fbd
h_sapiens_asm.ebwt.2.zip: Part 2   1.0 GB
MD5: c3485ec4572d0ce4bf658314594aba14
h_sapiens_37_asm.ebwt.zip: H. sapiens, NCBI 37.1   2.7 GB
MD5: ce6db52f78a8bfe3f3353da17430a71c
h_sapiens_37_asm.ebwt.1.zip: Part 1   1.7 GB
MD5: 22e6cd234c8ffdd7195d1bf773fd45c2
h_sapiens_37_asm.ebwt.2.zip: Part 2   1.0 GB
MD5: 2cc9d1150b2245251e22475b854064a2
mm9.ebwt.zip: M. musculus, UCSC mm9   2.4 GB
MD5: ca3801d768e80a60aa09eede83833b2f
mm9.ebwt.1.zip: Part 1   1.5 GB
MD5: e575e01588bfdc35d3e194863a69aa15
mm9.ebwt.2.zip: Part 2   905 MB
MD5: cc1e686038bf9ca46fa7fafcc3262a86
m_musculus_ncbi37.ebwt.zip: M. musculus, NCBI 37.1   2.4 GB
MD5: cba88978363aa274312f0e7ff1853d69
m_musculus_ncbi37.ebwt.1.zip: Part 1   1.5 GB
MD5: 90af7e7a75f3ae07c5e20aeb84306812
m_musculus_ncbi37.ebwt.2.zip: Part 2   905 MB
MD5: b81eed3027ac562f23aa606e008d5d49
b_taurus.ebwt.zip: B. taurus, UMD 3.0   2.1 GB
MD5: f15c1dfaa63dc85c7e072bf9ce7b07ef
b_taurus.ebwt.1.zip: Part 1   1.3 GB
MD5: a40d2edb7332535af93c32fa070a9bd5
b_taurus.ebwt.2.zip: Part 2   801 MB
MD5: b920a3b811a040f963d918ae14be8686
d_melanogaster_fb5_22.ebwt.zip: D. melanogaster, Flybase, r5.22   153 MB
MD5: c1a8c160bf5cd5c840c242ab0d38bc32
a_thaliana_tair9.ebwt.zip: A. thaliana, TAIR, TAIR9   119 MB
MD5: 903560fa325061163f44a65f7b572279
c_elegans_ws200.ebwt.zip: C. elegans, Wormbase, WS200   99 MB
MD5: f7821cf7aa7e119b9afd8724993b778e
s_cerevisiae.ebwt.zip: S. cerevisiae, CYGD   15 MB
MD5: bbd94e88708f7986ac65e3139f53f877
e_coli.ebwt.zip: E. coli, NCBI, st. 536   5.0 MB
MD5: 8a00d8b71f41157862b4719d6fb9aa6f