Site Map

News and Updates

    New releases and related tools will be announced through the Bowtie mailing list.

Getting Help

    Please use hisat2.genomics@gmail.com for private communications only. Please do not email technical questions to HISAT2 contributors directly.

Releases

Indexes (see note)

H. sapiens, GRCh38
genome 3.9 GB
genome_snp 4.6 GB
genome_tran 4.1 GB
genome_snp_tran 4.6 GB
H. sapiens, UCSC hg38
genome 4.1 GB
H. sapiens, UCSC hg38 and Refseq gene annotations referred to in the Nature Protocol paper
genome_tran 4.2 GB
H. sapiens, GRCh37
genome 3.9 GB
genome_snp 4.5 GB
genome_tran 4.0 GB
genome_snp_tran 4.5 GB
H. sapiens, UCSC hg19
genome 3.9 GB
M. musculus, GRCm38
genome 3.7 GB
genome_snp 4.0 GB
genome_tran 3.7 GB
genome_snp_tran 4.0 GB
M. musculus, UCSC mm10
genome 3.5 GB
R. norvegicus, UCSC rn6
genome 3.7 GB
D. melanogaster, BDGP6
genome 0.2 GB
genome_tran 0.2 GB
D. melanogaster, UCSC dm6
genome 0.2 GB
C. elegans, WBcel235
genome 0.1 GB
genome_tran 0.1 GB
C. elegans, UCSC ce10
genome 0.1 GB
S. cerevisiae, R64-1-1
genome 0.01 GB
genome_tran 0.01 GB
S. cerevisiae, UCSC sacCer3
genome 0.01 GB

* genome: HFM index for reference
* genome_snp: HGFM index for reference plus SNPs
* genome_tran: HGFM index for reference plus transcripts
* genome_snp_tran: HGFM index for reference plus SNPs and transcripts
more indexes

Related Tools

  • HISAT-genotype: Next-generation analysis of human genomes
  • HISAT: Fast and sensitive spliced alignment
  • Bowtie2: Ultrafast read alignment
  • TopHat2: Spliced read mapper for RNA-Seq
  • Cufflinks: Isoform assembly and quantitation for RNA-Seq
  • StringTie: Transcript assembly and quantification for RNA-Seq

Publications

Contributors

Links

Frequently Asked Questions