Bowtie 2 indexes

Bowtie 2 (GitHub repo) and Bowtie (GitHub repo) 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. Project home pages are Bowtie and Bowtie 2. HTTPS URLs allow you to download the files from your web browser or using command-line tools like wget or curl. Corresponding s3:// URLs can be derived from the HTTPS URLs (see the note before the download link definitions below) and are useful 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 / .bt2l 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. The Metadata column links to the archive MD5 file and, for newer builds, may also include a SAM-style sequence dictionary (.dict) and provenance manifest (.manifest.json).

Species/Build Source HTTPS URLs Metadata
Human / GRCh38 no-alt analysis set NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / GRCh38 no-alt +decoy set NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / GRCh38 + major SNVs NCBI+1KG1 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / GRCh37 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / Ash1v1.7 JHU 2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / Ash1v2.0 JHU 2 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / CHM13plusY T2T 3 full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / hs1 / T2T-CHM13v2.0 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Human / hg19 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Human / hg18 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Mouse / GRCm38 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Mouse / GRCm39 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Mouse / mm10 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Mouse / mm9 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Chimpanzee / Clint_PTRv2 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Chimpanzee / CHIMP2.1.4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Rhesus macaque / MMul_10 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Cow / ARS-UCD2.0 NCBI RefSeq full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Cow / ARS-UCD1.2 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Pig / Sscrofa11.1 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Dog / ROS_Cfam_1.0 NCBI RefSeq full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Dog / CanFam3.1 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Dog / CanFam4 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Rat / GRCr8 NCBI RefSeq full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Rat / rn4 UCSC full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Rat / Rnor6.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Chicken / bGalGal1.mat.broiler.GRCg7b NCBI RefSeq full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Chicken / GRCg6a NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Chicken / Galgal4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Zebrafish / GRCz11 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Zebrafish / GRCz10 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Corn / AGPv4 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Corn / B73 RefGenV5 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Wheat / IWGSC Ensembl Plants full zip, .1.bt2l, .2.bt2l, .3.bt2l, .4.bt2l, .rev.1.bt2l, .rev.2.bt2l archive md5, .dict, manifest json
Barley / MorexV3_pseudomolecules_assembly Ensembl Plants full zip, .1.bt2l, .2.bt2l, .3.bt2l, .4.bt2l, .rev.1.bt2l, .rev.2.bt2l archive md5, .dict, manifest json
Oryza sativa (rice) / IRGSP-1.0 Ensembl Plants full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5, .dict, manifest json
Oryza sativa (rice) / Build_4.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Arabidopsis thaliana / TAIR10 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Fruitfly / BDGP6 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Fruitfly / Dmel A4 1.0 NCBI full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
C. elegans / WBcel235 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
Yeast / R64-1-1 Ensembl full zip, .1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2 archive md5
  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.

Corresponding S3 URLs can be obtained by removing https://genome-idx.s3.amazonaws.com from the beginning of the URLs linked to above and replacing with s3://genome-idx.