## Site Map

- Home
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- Tools that use Bowtie

## Latest Release

Bowtie2 2.3.4.1 | 02/03/18
Please cite: Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

## Links

- Bowtie GitHub repository
- Report an issue

## Related Tools

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

## Indexes

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

H. sapiens, UCSC hg18 | 3.5 GB
or: part 1 (1.5 GB), part 2 (651 MB), part 3 (1.5 GB)
H. sapiens, UCSC hg19 | 3.5 GB
or: part 1 (1.5 GB), part 2 (650 MB), part 3 (1.5 GB)
H. sapiens, NCBI GRCh38 | 3.5 GB
M. musculus, UCSC mm10 | 3.2 GB
or: part 1 (1.3 GB), part 2 (600 MB), part 3 (1.3 GB)
M. musculus, UCSC mm9 | 3.2 GB
or: part 1 (1.3 GB), part 2 (593 MB), part 3 (1.3 GB)
R. norvegicus, UCSC rn4 | 3.1 GB
or: part 1 (1.3 GB), part 2 (580 MB), part 3 (1.3 GB)

Some unzip programs cannot handle archives >2 GB. If you have problems downloading or unzipping a >2 GB index, try downloading in parts.

## Related publications

- Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.
- 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.

## Contributors

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

## Related links

- Papers citing Bowtie 2
- Johns Hopkins University
- JHU Computer Science