GSNAP protocols

GSNAP specifications

Information


Unique identifier OMICS_00665
Name GSNAP
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

Versioning


Add your version

Maintainer


  • person_outline Thomas Wu <>

Publication for GSNAP

GSNAP IN pipelines

 (45)
2018
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 [44]. all fastq files were aligned to drosophila melanogaster genome (dmel-r6.18) using gsnap [45]. featurecounts [46,47] was used to assign reads to each gene using gtf file (dmel-all-r6.18.gtf) downloaded from flybase.org. we used r package deseq2 [48] to normalize reads, calculate […]

2018
PMCID: 5946439
PMID: 29747585
DOI: 10.1186/s12864-018-4735-5

[…] light type or waveband exposures were identified as detailed previously [16–20]. briefly, the trimmed and filtered reads are mapped to the xiphophorus cdna reference sequences (ensembl) [28] using gsnap [29]. mapped reads are quantified as raw counts in each file by xepress. differentially expressed genes were analyzed using the r-bioconductor package edger [30]. for a gene […]

2017
PMCID: 5241115
PMID: 28094001
DOI: 10.7554/eLife.19671.032

[…] cancer-related genes. libraries were sequenced on the illumina miseq platform for a targeted depth of no less than 500x for any individual amplicon. a custom-built bioinformatics pipeline utilizing gsnap for sequence alignment and freebayes for variant calling was employed for data analysis. all genomic regions were verified to be covered by at least 500 sequencing reads and identified variants […]

2017
PMCID: 5356070
PMID: 28300078
DOI: 10.1038/ncomms14752

[…] with a quality below q10, ensuring a minimum length of 20 bp remaining. reads were subsequently mapped to v3 of the maize b73 reference genome (http://ftp.maizesequence.org/b73_refgen_v3/) using gsnap 2.0.0 (ref. 49). the concordantly paired reads that uniquely map to the genome were used for quantification on the gene level with htseq-count from the htseq.py python package50., these genes […]

2017
PMCID: 5445603
PMID: 28573215
DOI: 10.1089/crpc.2016.0017

[…] src, stk11, and tp53. libraries were sequenced on the illumina miseq platform for a targeted depth of no less than 500 × for any individual amplicon. a custom-built bioinformatics pipeline utilizing gsnap for sequence alignment and freebayes for variant calling was employed for data analysis. all genomic regions were verified to be covered by at least 500 sequencing reads, and identified […]

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

GSNAP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GSNAP