Thanks to the AWS Open Data Sponsorship Program, indexes are freely available via HTTPS and S3.
Browse by tool
Kraken/Bracken
Indexes for Kraken 1/2, Bracken and related metagenomics tools.
Bowtie
Bowtie 1 & 2 reference indexes.
Movi
Movi 1/2 pangenome indexes.
HISAT
HISAT2 and related splice-aware aligner indexes.
Centrifuge
Centrifuge compact indexes for metagenomics classification.
SPUMONI
SPUMONI 1 compressed pangenome indexes for classification.
SPUMONI 2
SPUMONI 2 compressed pangenome indexes for classification.
From within AWS, e.g. from an EC2 instance, you can use the AWS CLI and its s3 co or s3 sync commands like this:
aws s3 cp s3://genome-idx/bt/grch38_1kgmaj.zip .
You can also initiate transfers using the AWS console, the Python boto3 library, and various other tools and libraries.
Access to files in the AWS Open Data Sponsorship Program is free. This is true whether you use the HTTPS or the S3 URL. For S3 URLs, the transfer is free even if it crosses an AWS region boundary; there is no inter-regional data transfer fee.