HISAT2 statistics

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HISAT2 specifications


Unique identifier OMICS_31397
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data SAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Perl, Python, Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.1.0
Stability Stable
Maintained Yes




No version available



  • person_outline HISAT2 Team

Additional information


Publication for HISAT2

HISAT2 citations


Basic leucine zipper transcription factor SlbZIP1 mediates salt and drought stress tolerance in tomato

BMC Plant Biol
PMCID: 5941487
PMID: 29739325
DOI: 10.1186/s12870-018-1299-0
call_split See protocol

[…] . The clean reads were filtered from the raw reads by removing duplication sequences, adaptor sequences and low-quality reads. Cleaned reads were subsequently mapped to the tomato reference genome by HISAT2 software []. The quantitative information of the RNA-seq data can be seen in Additional file : Table S3. Gene expression abundance was analyzed using StringTie software [], to identify DEGs (di […]


Systemic inhibition of the membrane attack complex impedes neuroinflammation in chronic relapsing experimental autoimmune encephalomyelitis

PMCID: 5932802
PMID: 29724241
DOI: 10.1186/s40478-018-0536-y
call_split See protocol

[…] Reads were trimmed using Trimmomatic [] (v0.32) and subsequently aligned against the mm10 reference genome using HISAT2 [] (v2.0.4) applying default parameters. Counts were obtained using the Ensembl GRCm38 GTF (v87) with HTSeq [] (v0.6.1). Quality checks were performed with FastQC (https://www.bioinformatics.ba […]


Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions

BMC Genomics
PMCID: 5930751
PMID: 29716520
DOI: 10.1186/s12864-018-4697-7

[…] For RNA-Seq, the raw reads were aligned to the hg19 reference assembly using HISAT2 with default options for alignment and the ‘—no-unal’ option was used to write only the aligned reads to the output file. RSEM [] was used for transcript assembly and abundance estimation. The […]


In depth comparative analysis of malaria parasite genomes reveals protein coding genes linked to human disease in Plasmodium falciparum genome

BMC Genomics
PMCID: 5930813
PMID: 29716542
DOI: 10.1186/s12864-018-4654-5

[…] complexity, low quality, and multiple Ns were filtered out. Duplicated reads were also removed. Thereafter, the resulting clean reads were mapped against the P. falciparum genome (PlasmoDB v26) using HISAT2 []. The abundance of each reference gene was estimated with StringTie []. Relative transcriptional activity of each euchromatic gene was assessed using transcripts per million (TPM). When TPM < […]


Transcriptional analysis of liver from chickens with fast (meat bird), moderate (F1 layer x meat bird cross) and low (layer bird) growth potential

BMC Genomics
PMCID: 5930858
PMID: 29716547
DOI: 10.1186/s12864-018-4723-9
call_split See protocol

[…] Reads were returned in fastq format. FastQC and adaptor sequences were trimmed from the 3′ end of reads with Cutadapt []. Hisat2 [] was used to map reads to the reference genome Galgal5.0 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Gallus_gallus). Duplicate reads were then removed. Stringtie [] was used to define the transcripts […]


Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] onia nodules, RNA was sequenced from the three nodule stages described earlier as well as uninoculated roots (SI Appendix, Table S8). RNA-seq reads were mapped to the Parasponia reference genome with HISAT2 version 2.02 () using an index that includes exon and splice site information in the RNA-seq alignments. Mapped reads were assigned to transcripts with featureCounts version 1.5.0 (). Normaliza […]


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HISAT2 institution(s)
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
HISAT2 funding source(s)
Supported in part by the National Human Genome Research Institute (US National Institutes of Health) under grants R01-HG006102 and R01-HG006677.

HISAT2 review

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Arup Ghosh

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HISAT2 the successor of HISAT is a fast and very accurate read aligner for RNA-seq experiments. Like the Tophat2 form Tuxedo pipeline, it takes care of spliced junctions as well.