Please cite:

Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019). https://doi.org/10.1038/s41587-019-0201-4

Index

HISAT2 indexes are hosted on AWS (Amazon Web Services), thanks to the AWS Public Datasets program. Click this link for more details.

H. sapiens

  • GRCh38
    • genome https://genome-idx.s3.amazonaws.com/hisat/grch38_genome.tar.gz
    genome_snp https://genome-idx.s3.amazonaws.com/hisat/grch38_snp.tar.gz
    genome_tran https://genome-idx.s3.amazonaws.com/hisat/grch38_tran.tar.gz
    genome_snp_tran https://genome-idx.s3.amazonaws.com/hisat/grch38_snptran.tar.gz
    genome_rep(above 2.2.0) https://genome-idx.s3.amazonaws.com/hisat/grch38_rep.tar.gz
    genome_snp_rep(above 2.2.0) https://genome-idx.s3.amazonaws.com/hisat/grch38_snprep.tar.gz
  • UCSC hg38
    • genome https://genome-idx.s3.amazonaws.com/hisat/hg38_genome.tar.gz
    genome_tran https://genome-idx.s3.amazonaws.com/hisat/hg38_tran.tar.gz
  • GRCh37
    • genome https://genome-idx.s3.amazonaws.com/hisat/grch37_genome.tar.gz
    genome_snp https://genome-idx.s3.amazonaws.com/hisat/grch37_snp.tar.gz
    genome_tran https://genome-idx.s3.amazonaws.com/hisat/grch37_tran.tar.gz
    genome_snp_tran https://genome-idx.s3.amazonaws.com/hisat/grch37_snptran.tar.gz
  • UCSC hg19
    • genome https://genome-idx.s3.amazonaws.com/hisat/hg19_genome.tar.gz

    M. musculus

  • GRCm38
    • genome https://cloud.biohpc.swmed.edu/index.php/s/grcm38/download
    genome_snp https://cloud.biohpc.swmed.edu/index.php/s/grcm38_snp/download
    genome_tran https://cloud.biohpc.swmed.edu/index.php/s/grcm38_tran/download
    genome_snp_tran https://cloud.biohpc.swmed.edu/index.php/s/grcm38_snp_tran/download
  • UCSC mm10
    • genome https://genome-idx.s3.amazonaws.com/hisat/mm10_genome.tar.gz

    R. norvegicus

  • UCSC rn6
    • genome https://genome-idx.s3.amazonaws.com/hisat/rn6_genome.tar.gz

    D. melanogaster

  • BDGP6
    • genome https://genome-idx.s3.amazonaws.com/hisat/bdgp6.tar.gz
    genome_tran https://genome-idx.s3.amazonaws.com/hisat/bdgp6_tran.tar.gz
  • UCSC dm6
    • genome https://genome-idx.s3.amazonaws.com/hisat/dm6.tar.gz

    C. elegans

  • WBcel235
    • genome https://genome-idx.s3.amazonaws.com/hisat/wbcel235.tar.gz
    genome_tran https://genome-idx.s3.amazonaws.com/hisat/wbcel235_tran.tar.gz
  • UCSC ce10
    • genome https://cloud.biohpc.swmed.edu/index.php/s/bbynxoY2TPpRNQb/download

    S. cerevisiae

  • R64-1-1
    • genome https://cloud.biohpc.swmed.edu/index.php/s/JRSoKHD5cHfpCFE/download
    genome_tran https://cloud.biohpc.swmed.edu/index.php/s/akeiMrGGtt5KoJY/download
  • UCSC sacCer3
    • genome https://cloud.biohpc.swmed.edu/index.php/s/Gsq4goLW4TDAz4E/download
    		 
    genome: HISAT2 index for reference
genome_snp: HISAT2 Graph index for reference plus SNPs
genome_tran: HISAT2 Graph index for reference plus transcripts
genome_snp_tran: HISAT2 Graph index for reference plus SNPs and transcripts

    Binaries

    Version: HISAT2 2.2.1

    Release Date: 7/24/2020
    Sourcehttps://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download
    OSX_x86_64https://cloud.biohpc.swmed.edu/index.php/s/zMgEtnF6LjnjFrr/download
    Linux_x86_64https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download

    Version: HISAT2 2.2.0

    Release Date: 2/6/2020
    Sourcehttps://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download
    OSX_x86_64https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-OSX_x86_64/download
    Linux_x86_64https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-Linux_x86_64/download

    Version: HISAT2 2.1.0

    Release Date: 6/8/2017
    Sourcehttps://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-source/download
    OSX_x86_64https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-OSX_x86_64/download
    Linux_x86_64https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-Linux_x86_64/download
    Windowshttp://www.di.fc.ul.pt/~afalcao/hisat2_windows.html