HISAT2 and HISAT-genotype indexes
HISAT2 (GitHub repo) is a fast splice-aware aligner for mapping sequencing reads to genomes and transcriptomes. This page lists prebuilt 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.