GSNAP pipeline

GSNAP specifications


Unique identifier OMICS_00665
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format SAM
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Thomas Wu <>

Publication for GSNAP

GSNAP citations

PMCID: 5943033

[…] using quick-rna microprep kit (r1050 zymo research). sequencing was performed on llumina hiseq2500 in 2 × 75 bp paired-end mode. reads were splice-aligned to the zebrafish genome, grcz10, using gsnap and known splice sites from ensembl gene annotation, version 81. featurecounts was used to assign reads to exons thus eventually getting counts per gene. edger package of r (robinson et al., […]

PMCID: 5754767

[…] tumor and matched normal tissues for whole-exome sequencing. total rna was extracted from cells for rna-sequencing. data generated with hiseq2500 (illumina) were aligned to the mouse genome using gsnap (34). for whole-exome sequencing, somatic single-nucleotide variants (snv) and insertion/deletions (indel) were called using strelka 1.0.4 (35). protein altering mutations include nonsynonymous […]

PMCID: 5547544

[…] using fastqc [37]. the resulting fragments were mapped to a blueberry draft genome [31] using gsnap version 2016–04-04 [38] allowing a maximum of 10% mismatches in each read. the algorithm in gsnap allows detection of complex variants involving multiple mismatches, long indels, and splicing in short reads, accepting user-provided databases of known exon–intron boundaries. this approach […]

PMCID: 5484669

[…] lanes on illumina hiseq2000 using 100 bp paired-end protocol., for each cell, paired-end reads were mapped to the m. musculus genome (grcm38) using genomic short-read nucleotide alignment program (gsnap) with default parameters52. next, uniquely mapped reads to the genome were counted using htseq-count ( and normalized with size factors using […]

PMCID: 5608509

[…] libraries were multiplexed and then sequenced on illumina hiseq2500 to generate 30m of single end 50 base pair reads. sequencing reads were mapped to the reference mouse genome (grcm38), using the gsnap short read aligner (wu and nacu, 2010). expression was measured in reads per kilobase per million total reads (rpkm). analysis of processed rnaseq data (normalized and variance-stabilized […]

GSNAP institution(s)
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA

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