| New releases and related tools will be announced through the Bowtie mailing list. |
| Please use hisat2.genomics@gmail.com for private communications only. Please do not email technical questions to HISAT2 contributors directly. |
| version 2.1.0 | 6/8/2017 |
| Source code | |
| Linux x86_64 binary | |
| Mac OS X x86_64 binary | |
| Windowns binary |
Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods
2015| 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 | |
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