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GSNAP specifications


Unique identifier OMICS_00665
Software type Application/Script
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


No version available


  • person_outline Thomas Wu

Additional information

Publication for GSNAP

GSNAP citations


CLIP related methodologies and their application to retrovirology

PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] s or transcriptomes. The most commonly used mapping algorithms used for this task include Bowtie [], Bowtie2 [], STAR [], Novoalign (, RMAP [], TopHat [], GSnap [], SOAP [] and BWA [], some with unique advantages over others depending on whether mapping is done on a genome versus transcriptome. The choice of algorithm and the parameters for mapping will […]


Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

BMC Genomics
PMCID: 5922311
PMID: 29695257
DOI: 10.1186/s12864-018-4675-0

[…] eads were removed before further analysis. The quality of the resulting reads was verified using FASTQC ( Alignment was done to galGal4 using GSNAP and gene expression was quantified using featureCounts and Ensembl release 79. The two technical replicates were averaged and differential expression analysis was done using the GLM method in ed […]


Brain Transcriptomic Analysis of Hereditary Cerebral Hemorrhage With Amyloidosis Dutch Type

PMCID: 5908973
PMID: 29706885
DOI: 10.3389/fnagi.2018.00102

[…] sing Sickle (RRID:SCR_006800, v1.33) with default settings. Adapter clipping was performed using Cutadapt (RRID:SCR_011841, v1.9.1) with default settings. RNA-Seq reads’ alignment was performed using GSNAP (RRID:SCR_005483, v2014-12-23) with setting “–npaths 1” on GRCh38 reference genome without the alternative contigs. The gene read quantification was performed using HTSeq-count (RRID:SCR_011867, […]


Full length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing

Genome Biol
PMCID: 5877393
PMID: 29598823
DOI: 10.1186/s13059-018-1418-0

[…] accurate transcription reconstruction is not feasible for short-read RNA-seq data, the comparison is made at the gene level using GENCODE annotation (version 19). As part of the GENTRAP pipeline [], GSNAP aligner with default parameters was used to align paired-end Illumina reads to the human genome (hg19). Next, HTSeq [] with default parameters was used to calculate the fragment counts per gene, […]


Homozygous KSR1 deletion attenuates morbidity but does not prevent tumor development in a mouse model of RAS driven pancreatic cancer

PLoS One
PMCID: 5875795
PMID: 29596465
DOI: 10.1371/journal.pone.0194998
call_split See protocol

[…] PA). The libraries were multiplexed and then sequenced on HiSeq4000 (Illumina) to generate ~30 million single end 50 base pair reads.RNASeq reads were aligned to the human genome version GRCh38 using GSNAP. Expression counts per gene were obtained by counting the number of reads aligned concordantly within a pair and uniquely to each gene locus as defined by NCBI and Ensembl gene annotations and R […]


Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] d into transcripts using both de novo and genome-guided methods (jaccard_clip option on) in Trinity v2.3.2 []. For the genome-guided method, RNA-seq reads were first aligned to the genome assembly by GSNAP v.2014.7.21 [] to generate a BAM file as the input. The resulting transcripts from these two modes were combined and aligned to the genome assembly with GMAP v.2014.7.21 [] incorporated in Progr […]


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

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