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JBrowse specifications

Information


Unique identifier OMICS_00918
Name JBrowse
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Ian H Holmes

Additional information


https://github.com/GMOD/jbrowse/wiki

Information


Unique identifier OMICS_00918
Name JBrowse
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Javascript, Perl, Python, Shell (Bash)
License Artistic License version 2.0, GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.14.2
Stability Stable

Versioning


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Additional information


https://github.com/GMOD/jbrowse/wiki

Publications for JBrowse

JBrowse citations

 (140)
library_books

Enhanced JBrowse plugins for epigenomics data visualization

2018
BMC Bioinformatics
PMCID: 5921565
PMID: 29699480
DOI: 10.1186/s12859-018-2160-z

[…] enome browsers are able to properly visualize these specialized data sets. Current genome browsers such as UCSC genome browser [], AnnoJ [], IGV [], WashU EpiGenome Browser [], Epiviz [], IGB [], and JBrowse [], have limited capability to visualize these data sets effectively, hindering the visualization and potential discoveries with new sequencing technologies. JBrowse is used by numerous scient […]

library_books

SNPversity: a web based tool for visualizing diversity

2018
PMCID: 5912076
PMID: 29688387
DOI: 10.1093/database/bay037

[…] pjack (), but stand-alone web-based visualization tools that can be easily implemented at web-based biological databases are not common, and SNPs are usually displayed through genome browsers such as JBrowse () or Ensembl genome browser (). Consequently, their display capabilities are limited and not specialized. The stand-alone SNPversity software suite was developed at MaizeGDB to respond to the […]

library_books

Ginseng Genome Database: an open access platform for genomics of Panax ginseng

2018
BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] Under the ‘Tools’ panel, ‘JBrowse’ was included to visualize the genomic features of ginseng. All of the assembled scaffolds and the predicted genes were used in constructing the genome browser. The main page of ‘JBrowse’ cont […]

library_books

High throughput detection of RNA processing in bacteria

2018
BMC Genomics
PMCID: 5870498
PMID: 29587634
DOI: 10.1186/s12864-018-4538-8

[…] ed well with both TSS and sites of major RNA processing as determined by dRNA-Seq and pRNA-Seq respectively. Statistics on the size and composition of each library can be viewed in Table . For online Jbrowse access to our data sets see www.pseudomonas.com […]

library_books

A genome wide identification and comparative analysis of the lentil MLO genes

2018
PLoS One
PMCID: 5865747
PMID: 29570745
DOI: 10.1371/journal.pone.0194945

[…] rches carried out on the protein NCBI datasets of the M. truncatula, chickpea, and common bean genomes. The MLO annotations in the lentil draft genome assembly v1.2 can be accessed through the lentil JBrowse or BLAST function at http://knowpulse.usask.ca. […]

library_books

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

2018
Front Plant Sci
PMCID: 5869928
PMID: 29616069
DOI: 10.3389/fpls.2018.00362

[…] each marker was estimated by r2. Associations were considered significant when p ≤ 0.0001 or LOD scores greater than 4.0. Finally, the biological function of the associated markers was identified in JBrowse environment from Sol Genomics Network (SGN) (Fernandez-Pozo et al., ) using tomato genome version SL2.40 and the ITAG annotation version 2.4. […]

Citations

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JBrowse institution(s)
Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA
JBrowse funding source(s)
Supported by the National Institutes of Health/National Human Genome Research Institute (R01-HG004483).

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