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HISAT specifications


Unique identifier OMICS_07225
Alternative name Hierarchical Indexing for Spliced Alignment of Transcript
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Perl, Python, Shell (Bash)
License GNU Affero General Public License version 3
Computer skills Advanced
Version 1.06
Stability Beta
Maintained Yes




No version available


  • person_outline Ben Langmead
  • person_outline Daehwan Kim

Publication for Hierarchical Indexing for Spliced Alignment of Transcript

HISAT citations


Neuropilin 1 promotes the oncogenic Tenascin C/integrin β3 pathway and modulates chemoresistance in breast cancer cells

BMC Cancer
PMCID: 5935908
PMID: 29728077
DOI: 10.1186/s12885-018-4446-y

[…] equencing reads were generated upon sequencing. The count per million (CPM) method was utilized for filtering low counts/noise by NOISeq. The clean reads were mapped to the reference genome using the HISAT []/ Bowtie2 tool []. The fragments per kilobase of transcript per million mapped reads (FPKM) method was utilized to calculate the expression levels. A false detection rate (FDR) ≤ 0.001 and the […]


Ginseng Genome Database: an open access platform for genomics of Panax ginseng

BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] s using SortMeRNA []. Finally, the low-quality reads were removed using NGS QC Toolkit []. The high-quality RNA-Seq reads were used for de novo assembly by Trinity [] and reference-guided assembly by HISAT & stringtie [] and then for gene prediction on the draft genome sequence. In addition, high quality PacBio sequences were used to refine the predicted gene models. […]


A Key Gene, PLIN1, Can Affect Porcine Intramuscular Fat Content Based on Transcriptome Analysis

PMCID: 5924536
PMID: 29617344
DOI: 10.3390/genes9040194

[…] is more than 50% in a read), adapter-polluted, and high content of unknown base (N) reads (more than 5%) from raw reads. Then, clean reads were aligned to the pig reference genome (Sscrofa10.2) using HISAT []. Sample transcripts were reconstructed using StringTie [], then reconstructed transcripts were compared to the reference annotation using Cuffcompare []. Coding potential of novel transcripts […]


Identification and Characterization of als Genes Involved in D Allose Metabolism in Lineage II Strain of Listeria monocytogenes

Front Microbiol
PMCID: 5893763
PMID: 29670595
DOI: 10.3389/fmicb.2018.00621
call_split See protocol

[…] ording to the sequencing procedure used by the Beijing Genomics Institute (BGI, China). After filtering out low quantity sequences, clean reads were generated and mapped to the reference genome using HISAT and Bowtie2 tools (Langmead et al., ; Kim et al., ). The Poisson distribution method was used to analyze differentially expressed genes (DEGs). Clustering analysis of DEGs was performed with clu […]


QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA seq data

Genome Biol
PMCID: 5874996
PMID: 29592814
DOI: 10.1186/s13059-018-1414-4

[…] 0 million paired-end reads. Each method was then run twice on all four samples and the run times were averaged. For Roar, DaPars, and GETUTR, reads were first aligned to the mouse genome (mm10) using HISAT []. Where the methods used parallel computing, multiprocessing was enabled using eight threads. All computation was carried out on a cluster equipped with four Intel Xeon E7–4830 2.13 Ghz 8-core […]


Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold tolerance of rubber tree

Sci Rep
PMCID: 5862945
PMID: 29563566
DOI: 10.1038/s41598-018-23094-y

[…] 74.74 Mb (A2), 74.12 Mb (B0), 74.15 Mb (B1), and 74.39 Mb (B2) of clean reads (Table ) (NCBI accession numbers: GSE67559). These high-quality clean reads were then mapped to the reference genome use HISAT (Hierarchical indexing for spliced alignment of transcripts). On average, 89.87% of the reads were mapped onto the rubber tree genome for each sample, suggesting that the samples were comparable […]


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HISAT 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
HISAT 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.

HISAT review

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Arup Ghosh

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Hisat is one of the best and fastest RNA-seq data aligner available till date. Mouse transcriptome data with ~30 million reads took only 30mins for alignment. There are a lot other alignment-free alternatives available now but for getting insight about spliced variants Hisat is the best tool to use.