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

Abstract

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.

Authors:
 [1];  [1];  [2];  [3];  [4];  [4];  [3];  [2];  [4];  [5]; ORCiD logo [6]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering
  2. Univ. of Missouri, Columbia, MO (United States). Division of Animal Sciences
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Ontario Inst. of Cancer Research, Toronto, ON (Canada); Univ. of Toronto, ON (Canada). Dept. of Molecular Genetics
  6. Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE; National Inst. of Health (NIH) (United States)
OSTI Identifier:
1456937
Grant/Contract Number:  
AC02-05CH11231; HG004483; GM080203
Resource Type:
Accepted Manuscript
Journal Name:
Genome Biology (Online)
Additional Journal Information:
Journal Name: Genome Biology (Online); Journal Volume: 17; Journal ID: ISSN 1474-760X
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; genome; browser; bioinformatics

Citation Formats

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, and Holmes, Ian H. JBrowse: a dynamic web platform for genome visualization and analysis. United States: N. p., 2016. Web. doi:10.1186/s13059-016-0924-1.
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. JBrowse: a dynamic web platform for genome visualization and analysis. United States. doi:10.1186/s13059-016-0924-1.
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, and Holmes, Ian H. Tue . "JBrowse: a dynamic web platform for genome visualization and analysis". United States. doi:10.1186/s13059-016-0924-1. https://www.osti.gov/servlets/purl/1456937.
@article{osti_1456937,
title = {JBrowse: a dynamic web platform for genome visualization and analysis},
author = {Buels, Robert and Yao, Eric and Diesh, Colin M. and Hayes, Richard D. and Munoz-Torres, Monica and Helt, Gregg and Goodstein, David M. and Elsik, Christine G. and Lewis, Suzanna E. and Stein, Lincoln and Holmes, Ian H.},
abstractNote = {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.},
doi = {10.1186/s13059-016-0924-1},
journal = {Genome Biology (Online)},
number = ,
volume = 17,
place = {United States},
year = {2016},
month = {4}
}

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