Bowtie 2

Fast and sensitive read alignment

Site Map

Latest Release

Bowtie2 2.3.1 03/04/17 

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

Links

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

Contributors

Related links

Tools that use Bowtie 1 and/or 2:

OS distributions with Bowtie packages

Commercial products using Bowtie:

Published protocols using Bowtie 1 and/or 2: