HISAT pipeline

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



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  • person_outline Ben Langmead <>
  • person_outline Daehwan Kim <>

Publication for Hierarchical Indexing for Spliced Alignment of Transcript

HISAT IN pipelines

PMCID: 5833345
PMID: 29352142
DOI: 10.1038/s41419-017-0066-8

[…] raw sequencing reads were filtered to remove reads with adapters, reads in which unknown bases are more than 10%, and low quality reads. clean reads were then obtained and stored as fastq format. hisat45 was used to map clean reads to the genome of hg19. gene expression levels are quantified by a software package called rsem46. noiseq method47 was used to screen differentially expressed genes […]

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

[…] 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 [14]/ bowtie2 tool [15]. 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 […]

PMCID: 5315355
PMID: 28212420
DOI: 10.1371/journal.pone.0172478

[…] draft genome sequences as a reference to map our sequencing clean reads. and gene model annotation files of relative species were downloaded from genome website (http://gigadb.org/dataset/100186). hisat (v2.0.14) was used to index reference draft genome sequence [15]. software tophat (v2.0.9) was used to aligne clean data to reference genome and identify splice variants of each sample [16, […]

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.