GMAP protocols

GMAP specifications

Information


Unique identifier OMICS_15072
Name GMAP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-01-14.tar.gz
Maintained Yes

Download


Versioning


Add your version

Maintainer


  • person_outline Thomas Wu <>

Publication for GMAP

GMAP IN pipelines

 (17)
2017
PMCID: 5550469
PMID: 28794490
DOI: 10.1038/s41598-017-08138-z

[…] in aid of illumina short reads using lordec tool v0.6 with -k 21, -s 3, and default setting for other parameters23., the corrected isoform sequences were aligned against reference genome using gmap aligner v2016-08-2427 with the parameters: –min-identity 0.95 and –allow-close-indels 2. the sequences with multiple and chimeric alignments were excluded from the following analyses. among raw […]

2017
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] protocol (metrichor, oxford, uk) after which fastq sequences were extracted with poretools v0.6.0 [33] according to the “best” protocol. sequencing reads were aligned to the human genome (hg19) with gmap v2016-06-30 [53] to account for splicing events. wild-type (wt), nonsense, and rescue alleles were quantified with rsamtools v1.26.0 for aligned sequences [36], and with gmap splicesites output […]

2017
PMCID: 5563332
PMID: 28447221
DOI: 10.1007/s00401-017-1714-x

[…] genome (hg19) with gmap v2016-06-30 [53] to account for splicing events. wild-type (wt), nonsense, and rescue alleles were quantified with rsamtools v1.26.0 for aligned sequences [36], and with gmap splicesites output for splicing events. the ptc expression fraction was calculated as (expressionnonsense/expressionnonsense+wt); 0% corresponds to complete degradation of ptc bearing […]

2017
PMCID: 5665505
PMID: 29091722
DOI: 10.1371/journal.pone.0185595

[…] [37]; (blastn; e-value: e-10; isotig coverage > = 10%). then, 454 reads were mapped to e. tef whole genome shotgun (wgs) sequences lapy01000001 to lapy01013883 [37], using the software gmap [38] (coverage > 80%; identity >85%)., a subgroup of sequences was also searched for chimeric assemblies. this subgroup comprised sequences of 3850–15244 bp in size, which included […]

2017
PMCID: 5681567
PMID: 29127278
DOI: 10.1038/s41467-017-01316-7

[…] were then interrogated for the presence of a poly(a) tail and one of 16 polyadenylation signal hexamer motifs (see supplementary table 6). the contigs were aligned to the genome assembly using gmap (v2016-05-01, -f samse, -t 20)60, and instances where there was a 3′ sequence mismatch due to a run of as, or a 5′ mismatch due to a run of ts (in cases where the strand specific sequencing […]

GMAP institution(s)
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA, USA; Department of Corporate Information Technology, Genentech, Inc, South San Francisco, CA, USA

GMAP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GMAP