## Site Map

- Home
- Manual
- FAQ

## 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

version 2.1.0 | 6/8/2017
Source code
Linux x86_64 binary
Mac OS X x86_64 binary
Windowns binary

Please cite:

Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods

2015

## 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

- Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015

- Pertea M, Kim D, Pertea G, Leek JT and Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols 2016

## Contributors

- Daehwan Kim
- Ben Langmead
- Joe Paggi
- Geo Pertea
- Steven Salzberg

## Links

- Center for Computational Biology at Johns Hopkins University
- Computer Science Department at Johns Hopkins University