GMAP pipeline

GMAP specifications


Unique identifier OMICS_15072
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Thomas Wu <>

Publication for GMAP

GMAP citations

PMCID: 5902842

[…] to the red5 whole genome sequence for purposes of assisting manual annotation. the cds for the ‘hongyang’ gene set of yue and colleagues [18] was aligned to the red5 whole genome sequence using gmap [31] (version 2017–06-20), the resultant gff3 output converted to simplified annotation format (saf) and rna-seq read counts to these features extracted using featurecounts [32]., of the 2034 […]

PMCID: 5498581

[…] were also used to extract the expression based exn50 measure. expression values for the assembled transcripts were measured using express or kallisto quantification tools. gmap was used to align the assembled transcripts against the reference genome and to measure the percentage identity of the aligned transcripts for isoforms of at least 200 bp., to measure […]

PMCID: 5563332

[…] 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 […]

PMCID: 4639833

[…] and paired-end contigs were aligned against the genome and annotation of european seabass (diclab1), nile tilapia (orenil1.1) and stickleback (gasterosterus aculeatus, broad v1.0) using the program gmap v13.8.1944 and snpdat v1.0.545 with default parameters. considering the divergence between asian seabass and each of the aforementioned three species, only loci with more than 70% of sequence […]

PMCID: 2753554

[…] unigene database at the ncbi , h-invdb database and fantom3 database . to identify putative transcribed pseudogenes, individual transcript sequences were mapped onto the respective genomes using gmap software [41] with match criteria of >99% sequence identity and >99% sequence coverage. transcript sequences that mapped to pseudogenes were aligned to parent protein sequences […]

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

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