Index zone

HTTPS and S3 links to genomic index files freely available in the AWS cloud

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Bowtie 2 indexes

Bowtie and Bowtie 2 are read aligners for sequencing reads. Bowtie specializes in short reads, generally about 50bp or shorter. Bowtie 2 specializes in longer reads, up to around hundreds of base pairs. HTTPS URLs allow you to download the files from your web browser or using command-line tools like wget or curl. The S3 URLs can be used with AWS tools, including the AWS console and AWS command-line interface.

In the past, Bowtie 1 & 2 had incompatible genome indexes. This changed in July 2019 when Bowtie v1.2.3 gained the ability to use Bowtie 2 formatted genome indexes (ending in .bt2). We list only Bowtie 2-format .bt2 index files here.

You can download all the files for a given assembly as a single zip file, or as 6 separate .bt2 files. For example, if you only need the forward version of the genome index (e.g. for exact matching only), you can download the files individually and omit the .rev.1.bt2 and .rev.2.bt2 files. Downloading already-decompressed index files might also be quicker for applications running in the AWS cloud.

Species/Build Source HTTPS URLs S3 URLs
Human / GRCh38 no-alt analysis set1 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / GRCh38 no-alt +decoy set1 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / GRCh38 + major SNVs NCBI+1KG2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / CHM13plusY T2T3 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / GRCh37 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / Ash2.0 JHU4 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / Ash1.7 JHU4 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / hg19 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Human / hg18 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Mouse / GRCm38 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Mouse / GRCm39 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Mouse / mm10 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Mouse / mm9 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Chimpanzee / Clint_PTRv2 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Chimpanzee / CHIMP2.1.4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Rhesus macaque / MMul_10 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Cow / ARS-UCD1.2 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Pig / Sscrofa11.1 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Dog / CanFam3.1 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Dog / CanFam4 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Rat / rn4 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Rat / Rnor6.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Chicken / GRCg6a NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Chicken / Galgal4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Zebrafish / GRCz11 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Zebrafish / GRCz10 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Corn / AGPv4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Corn / B73 RefGenV5 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Oryza sativa (rice) / Build_4.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Arabidopsis thaliana / TAIR10 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Fruitfly / BDGP6 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Fruitfly / Dmel A4 1.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
C. elegans / WBcel235 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
Yeast / R64-1-1 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2
  1. Before 10/29/2020, the index posted here erroneously included ALT loci. This was fixed on 10/29/2020.
  2. Major SNVs determined from 1000 Genomes Project variant calls. Details here.
  3. CHM13 human reference from Telomere-to-Telomere consortium, plus Y chromosome from GRCh38
  4. Ashkenazi reference genome from 10.1186/s13059-020-02047-7

Bowtie and Bowtie 2 are the work of Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg, Val Antonescu, Rone Charles among others. Please see the Bowtie and Bowtie 2 websites for more information on the software, authors, and how to cite the work.