GBrowse protocols

GBrowse specifications

Information


Unique identifier OMICS_00910
Name GBrowse
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format BAM,SAM
Operating system Unix/Linux, Mac OS
Programming languages Perl
License Artistic License version 2.0, GNU General Public License version 3.0
Computer skills Advanced
Version 2.56
Stability Stable
Requirements Apache
Source code URL https://metacpan.org/release/GBrowse
High performance computing Yes
Maintained Yes

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Maintainer


  • person_outline Lincoln D. Stein <>

Publications for GBrowse

GBrowse IN pipelines

 (53)
2017
PMCID: 5223126
PMID: 28071692
DOI: 10.1038/srep40121

[…] under the accession lwhd00000000. the version described in this paper is version lwhd01000000. the genome data can also be accessible through g-browser (http://bioinfo.konkuk.ac.kr/cgi-bin/gb2/gbrowse/krymar). the transcriptome shotgun assembly project has been deposited at ddbj/embl/genbank under the accession # genf00000000. the version described in this paper is the first version, […]

2017
PMCID: 5909465
PMID: 29149280
DOI: 10.1093/dnares/dsx045

[…] gene annotation (itag 2.4, downloaded from the solgenomics website), and the cor and luc genomes. gene annotations of cor, luc, and heinz, were included in species-specific partition in the gbrowse database. a download data section allows sequences and data to be accessed upon request. association of all the genes among the three genomes from each annotation (heinz 1706, cor and luc) […]

2016
PMCID: 4702478
PMID: 26779207
DOI: 10.3389/fpls.2015.01133

[…] furthermore, our thanks go the reviewers and the editor for their constructive and helpful suggestions and criticism., www.ncbi.nlm.nih.gov/tools/primer-blast , http://gb.sc.noble.org/cgi-bin/gb2/gbrowse/medicago_4/?name=chr1%3a37484310..37485662 , the supplementary material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fpls.2015.01133, table s1 | […]

2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] annotations as present on the coge database were used (solanum lycopersicum: id12289, solanum tuberosum: id16729, malus x domestica: id20240, capsicum annuum: id22828)., urls: , - globe artichoke gbrowse, http://gviewer.gc.ucdavis.edu/cgi-bin/gbrowse/artichoke_v1_1., - soiloco scripts, https://bitbucket.org/dscaglione/soiloco., accession codes: genome sequence data and annotation […]

2016
PMCID: 4726258
PMID: 26786968
DOI: 10.1038/srep19427

[…] used (solanum lycopersicum: id12289, solanum tuberosum: id16729, malus x domestica: id20240, capsicum annuum: id22828)., urls: , - globe artichoke gbrowse, http://gviewer.gc.ucdavis.edu/cgi-bin/gbrowse/artichoke_v1_1., - soiloco scripts, https://bitbucket.org/dscaglione/soiloco., accession codes: genome sequence data and annotation have been deposited on ncbi as wgs genome entry […]

GBrowse institution(s)
Ontario Institute for Cancer Research, Toronto, ON, Canada
GBrowse funding source(s)
Supported by grant #P41 G02223 from the National Human Genome Research Institute at the US National Institutes of Health, and by the Ministry of Economic Development and Innovation, Ontario (in part).

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