## Site Map

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- Tools that use Bowtie

## Latest Release

Bowtie 1.2.2 | 12/11/17
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.

## Links

- Bowtie GitHub repository
- Report an issue

## Related Tools

Bowtie 2: Fast, accurate read alignment
Crossbow: Genotyping, cloud computing
Tophat: RNA-Seq splice junction mapper
Cufflinks: Isoform assembly, quantitation
Myrna: Cloud, differential gene expression
Lighter: Fast error correction
Other tools using Bowtie

## 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, 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, 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, NCBI v37 | 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
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

- 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. Bioinformatics 2009 25(9):1105-1111.

## Contributors

- Ben Langmead
- Cole Trapnell
- Daehwan Kim
- Rone Charles
- Chris Wilks
- Valentin Antonescu

## Related links

- Papers citing Bowtie
- Johns Hopkins University
- JHU Computer Science