JBrowse: a dynamic web platform for genome visualization and analysis

Buels, Robert; Yao, Eric; Diesh, Colin M.; Hayes, Richard D.; Munoz-Torres, Monica; Helt, Gregg; Goodstein, David M.; Elsik, Christine G.; Lewis, Suzanna E.; Stein, Lincoln; Holmes, Ian H.

doi:10.1186/s13059-016-0924-1

Title: JBrowse: a dynamic web platform for genome visualization and analysis

Journal Article · Tue Apr 12 00:00:00 EDT 2016 · Genome Biology (Online)

DOI:https://doi.org/10.1186/s13059-016-0924-1· OSTI ID:1456937

Buels, Robert ^[1]; Yao, Eric ^[1]; Diesh, Colin M. ^[2]; Hayes, Richard D. ^[3]; Munoz-Torres, Monica ^[4]; Helt, Gregg ^[4]; Goodstein, David M. ^[3]; Elsik, Christine G. ^[2]; Lewis, Suzanna E. ^[4]; Stein, Lincoln ^[5];

^[6]

Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
Univ. of Missouri, Columbia, MO (United States). Division of Animal Sciences
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Ontario Inst. of Cancer Research, Toronto, ON (Canada); Univ. of Toronto, ON (Canada). Dept. of Molecular Genetics
Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Inst. of Health (NIH) (United States)

Grant/Contract Number:: AC02-05CH11231; HG004483; GM080203

OSTI ID:: 1456937

Journal Information:: Genome Biology (Online), Vol. 17; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 462 works

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Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula Lehmann, Robert; Lightfoot, Damien J.; Schubter, Celia Molecular Ecology Resources https://doi.org/10.1101/278267	journal	March 2018
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Evolution of the modular, disordered stress proteins known as dehydrins Riley, Andrew C.; Ashlock, Daniel A.; Graether, Steffen P. PLOS ONE, Vol. 14, Issue 2 https://doi.org/10.1371/journal.pone.0211813	journal	February 2019
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures. Collord, Grace; Tarpey, Patrick; Kurbatova, Natalja Springer Science and Business Media LLC https://doi.org/10.17863/cam.34814	journalarticle	January 2018
UVSSA, UBP12, and RDO2/TFIIS Contribute to Arabidopsis UV Tolerance Al Khateeb, Wesam M.; Sher, Annan A.; Marcus, Jeffery M. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00516	journal	April 2019
Genome-wide association mapping of date palm fruit traits Hazzouri, Khaled M.; Gros-Balthazard, Muriel; Flowers, Jonathan M. ETH Zurich https://doi.org/10.3929/ethz-b-000372739	text	January 2019
WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata. Putman, Timothy; Lelong, Sebastien; Burgstaller-Muehlbacher, Sebastian figshare https://doi.org/10.6084/m9.figshare.5150065	audiovisual	January 2017
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COSMIC: somatic cancer genetics at high-resolution Forbes, Simon A.; Beare, David; Boutselakis, Harry Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1121	journal	November 2016
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data Skrzypek, Marek S.; Binkley, Jonathan; Binkley, Gail Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw924	journal	October 2016
PopHuman: the human population genomics browser Casillas, Sònia; Mulet, Roger; Villegas-Mirón, Pablo Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx943	journal	October 2017
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology Arnaiz, Olivier; Meyer, Eric; Sperling, Linda Nucleic Acids Research https://doi.org/10.1093/nar/gkz948	journal	November 2019
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat Wang, Wenxi; Wang, Zihao; Li, Xintong GigaScience https://doi.org/10.1101/626705	journal	February 2020
Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima Rodríguez del Río, Álvaro; Minoche, André E.; Zwickl, Nikolaus F. The Plant Journal, Vol. 99, Issue 6 https://doi.org/10.1111/tpj.14413	journal	June 2019
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Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians An, Yang; Kawaguchi, Akane; Zhao, Chen Zoological Letters, Vol. 4, Issue 1 https://doi.org/10.1186/s40851-018-0102-2	journal	August 2018
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Genome-wide association mapping of date palm fruit traits Hazzouri, Khaled M.; Gros-Balthazard, Muriel; Flowers, Jonathan M. Nature Publishing Group https://doi.org/10.5167/uzh-182380	text	January 2019
Sugarcane ORF finder: the web-application for mining genes from sugarcane genome Kang, Yang Jae Plant Biotechnology Reports, Vol. 13, Issue 5 https://doi.org/10.1007/s11816-019-00574-9	journal	October 2019
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Using long-read sequencing to detect imprinted DNA methylation Gigante, Scott; Gouil, Quentin; Lucattini, Alexis Nucleic Acids Research https://doi.org/10.1101/445924	journal	January 2019
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Prediction of acute myeloid leukaemia risk in healthy individuals Abelson, Sagi; Collord, Grace; Ng, Stanley WK Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.30393	text	January 2018
The landscape of somatic mutation in normal colorectal epithelial cells. Lee-Six, Henry; Olafsson, Sigurgeir; Ellis, Peter Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.47346	text	January 2019
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The round goby genome provides insights into mechanisms that may facilitate biological invasions. Adrian-Kalchhauser, Irene; Blomberg, Anders; Larsson, Tomas BioMed Central https://doi.org/10.7892/boris.144050	text	January 2020
AML: Predicting the Unpredictable Takahashi, Koichi Cell Stem Cell, Vol. 23, Issue 2 https://doi.org/10.1016/j.stem.2018.07.005	journal	August 2018
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The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community Darde, Thomas A.; Lecluze, Estelle; Lardenois, Aurélie Bioinformatics, Vol. 35, Issue 17 https://doi.org/10.1093/bioinformatics/btz047	journal	January 2019
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The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2 Zhu, James; Kim, Jiwoong; Xiao, Xue BioRxiv https://doi.org/10.1101/2020.02.08.939553	journal	September 2020
Children???s Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools Shen, Lishuang; Maglinte, Dennis; Ostrow, Dejerianne BioRxiv https://doi.org/10.1101/2020.05.11.089763	journal	May 2020
De novo phased assembly of the Vitis riparia grape genome Girollet, Nabil; Rubio, Bernadette; Bert, Pierre-Francois Scientific Data https://doi.org/10.1101/640565	journal	May 2019
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Tasks, Techniques, and Tools for Genomic Data Visualization Nusrat, Sabrina; Harbig, Theresa; Gehlenborg, Nils arXiv https://doi.org/10.48550/arxiv.1905.02853	text	January 2019
EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts Lo, Chien-Chi; Shakya, Migun; Davenport, Karen arXiv https://doi.org/10.48550/arxiv.2006.08058	preprint	January 2020
IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee Genomics & Informatics, Vol. 15, Issue 4 https://doi.org/10.5808/gi.2017.15.4.178	journal	December 2017
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