JBrowse protocols

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JBrowse computational protocol

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


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Documentation


Maintainer


This tool is not maintained anymore.

Additional information


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

Publications for JBrowse

JBrowse IN pipelines

 (14)
2018
PMCID: 5759298
PMID: 29310588
DOI: 10.1186/s12864-017-4403-1

[…] 98,162 scaffolds and has been deposited at ddbj/ena/genbank under the accession peqf00000000. to obtain a more reasonable assembly for downstream bioinformatics analyses and for visualization in jbrowse [33], scaffolds were filtered with the following parameters: scaffolds were removed when they contained fewer than 800 bases, or when 90% of the total scaffold length was contained […]

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

[…] (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
PMID: 28465712
DOI: 10.1186/s13007-017-0181-7

[…] <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 […]

2017
PMCID: 5519730
PMID: 28729683
DOI: 10.1038/s41598-017-04768-5

[…] nucleotide reads were mapped to the annotated genome of strain ua159 (genbank accession: nc_004350.2). samtools software was used to divide the reads in each according strand. for visualization, jbrowse viewer was employed36. differential expression analyses of samples with and without xip were determined based on the mapped read profiles using a perl script. the read counts were subjected […]

2017
PMCID: 5730576
PMID: 29242500
DOI: 10.1038/s41598-017-17484-x

[…] (http://tree.bio.ed.ac.uk/software/figtree/)., the genome assembly, gene models, and protein models described in this study are available for download at http://spis.reefgenomics.org/download. a jbrowse genome browser is available at http://spis.reefgenomics.org/jbrowse. a blast server for the stylophora pistillata genome is available at http://spis.reefgenomics.org/blast/. raw sequence data […]

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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