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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:

“genome”: HISAT2 index for linear reference
“snp”: HISAT2 index for graph reference including SNPs
“tran”: HISAT2 index for reference plus annotated transcripts
“snp+tran”: HISAT2 index for reference including SNPs, plus annotated transcripts
“rep”: HISAT2 repeat index for reference
“snp+rep”: HISAT2 repeat index for reference including SNPs

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.