GSNAP protocols

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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


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  • person_outline Thomas Wu <>

Additional information

Publication for GSNAP

GSNAP in pipelines

PMCID: 5844946
PMID: 29523845
DOI: 10.1038/s41598-018-22701-2

[…] regions were trimmed using trim galore ( cleaned reads were aligned onto the complete latest human genome (assembly hg19) by means of gsnap version 2013-11-27 (using as parameters: -b 5 -d hg19 -t5 -s splicesites -e1000 -n1 -n1 -q -o–nofails -a sam–force-xs-dir -a paired) providing a list of exon-exon junctions from ensembl, ucsc […]

PMCID: 5852578
PMID: 29439397
DOI: 10.3390/genes9020082

[…] we downloaded 10 fastq files for 0–2 h and 11 fastq files for 6–8 h embryonic transcripts from modencode []. all fastq files were aligned to drosophila melanogaster genome (dmel-r6.18) using gsnap []. featurecounts [,] was used to assign reads to each gene using gtf file (dmel-all-r6.18.gtf) downloaded from we used r package deseq2 [] to normalize reads, calculate fold […]

PMCID: 5943033
PMID: 29624168
DOI: 10.7554/eLife.32965.027

[…] 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 () was used […]

PMCID: 5943425
PMID: 29573206
DOI: 10.1002/cam4.1439

[…] rather than true tumor progression., rna sequencing libraries were prepared using the illumina truseq rna library preparation kit v2. the sequenced reads were trimmed and mapped onto hg19 using gsnap version 2012‐12‐20 . the resulting aligned reads were summarized into bed files using samtools and bedtools (bamtobed version 2.16.2) . the bed files were used to estimate reads per kilobase […]

PMCID: 5946439
PMID: 29747585
DOI: 10.1186/s12864-018-4735-5

[…] due to light type or waveband exposures were identified as detailed previously [–]. briefly, the trimmed and filtered reads are mapped to the xiphophorus cdna reference sequences (ensembl) [] using gsnap []. mapped reads are quantified as raw counts in each file by xepress. differentially expressed genes were analyzed using the r-bioconductor package edger []. for a gene to be a differentially […]

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GSNAP in publications

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5921268
PMID: 29699483
DOI: 10.1186/s12862-018-1175-4

[…] sequencher® v5.1 (gene code corp, usa) []. whereas, the raw sequencing reads generated from ion torrent sequencing platform were assembled using genomics short-read nucleotide alignment program, gsnap [], integrated into sequencher® v5.2.4 []., multiple sequence alignment (msa) of the malaysian denv3/iii isolates along with denv3/iii sequences downloaded from genbank were aligned using […]

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

[…] 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 […]

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 […]

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

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