JBrowse pipeline

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

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Versioning


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Documentation


Maintainer


This tool is not maintained anymore.

Additional information


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

Publications for JBrowse

JBrowse citations

 (5)
2018
PMCID: 5763776

[…] the apache server handles queries from web clients through php scripts to perform searches. in the back-end part, all of the data in asgdb were stored and managed in mysql relational databases. the jbrowse genome browser is a combination of database and interactive web pages for manipulating and visualizing genes with large-scale sequence datasets [46, 47]. this next generation ajax-based […]

2018
PMCID: 5912076

[…] (7), 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 (3) or ensembl genome browser (4). consequently, their display capabilities are limited and not specialized. the stand-alone snpversity software suite was developed at maizegdb to respond […]

2017
PMCID: 5408436

[…] <1e−160, identity to query >70% and minimum sequence length of 200 residues). results were further curated manually by visual analysis of the blastp alignments and corresponding gene models in jbrowse (https://solgenomics.net/organism/nicotiana_benthamiana/genome) to eliminate potential partial protein due to mis-annotation. as a result, 36 additional candidates were retained for a total […]

2016
PMCID: 4950607

[…] the mapped reads were separated into the forward and reverse complement directions using the “mpileup” option of the samtools software [69]. the mapped reads on each strand were visualized in the jbrowse genome viewer [70] for sequencing quality., a custom computer script (miller et al., manuscript in preparation) was developed to detect and categorize srnas based on the single nucleotide rna […]

2015
PMCID: 4401323

[…] type elements (supplementary table s3). both the raw sequencing reads and assembled sequences have been submitted to ncbi, which has been supplemented by a pennycress genome database containing a jbrowse genome browser,47 blast database, and data repository available at pennycress.umn.edu., of the sequenced brassicaceae genomes, pennycress is most closely related to e. salsugineum, […]

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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