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

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HISAT2 and HISAT-genotype indexes

There are different types of indexes depending on whether transcripts and/or single-nucleotide variants are included in the graph index:

Indexes with rep in the name require HISAT2 v2.2.0 or above.

Species / Build FASTA source HTTPS URL S3 URL
Human / GRCh38 Ensembl genome, snp, tran, snp+tran, rep, snp+rep genome, snp, tran, snp+tran, rep, snp+rep
Human / hg38 UCSC genome, tran genome, tran
Human / GRCh37 NCBI genome, snp, tran, snp+tran genome, snp, tran, snp+tran
Human / hg19 UCSC genome genome
Mouse / GRCm38 NCBI genome, snp, tran, snp+tran genome, snp, tran, snp+tran
Mouse / mm10 UCSC genome genome
Rat / rn6 UCSC genome genome
Drosophila / BDGP6 Ensembl genome, tran genome, tran
Drosophila / dm6 UCSC genome genome
C. elegans / WBcel235 Ensembl genome, tran genome, tran

HISAT-genotype allele files

Species / Build HTTPs URLs S3 URLs
Human / GRCh38 genotypes genotypes

HISAT, HISAT2 and HISAT-genotype are the work of Daehwan Kim, Joe Paggi, Geo Pertea, Christopher Bennett, Yun (Leo) Zhang, Chanhee Park, Ben Langmead, Steven Salzberg among others. Please see the HISAT, HISAT2 and HISAT-genotype websites for more information on the software, authors, and how to cite the work.