JBrowse 2: a modular genome browser with views of synteny and structural variation

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. I...

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Vydáno v:Genome Biology Ročník 24; číslo 1; s. 74
Hlavní autoři: Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A., Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N., Haw, Robin, Cain, Scott, Buels, Robert M., Stein, Lincoln D., Holmes, Ian H.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 17.04.2023
Springer Nature B.V
BMC
Témata:
Animal Genetics and Genomics
Annotations
Bioinformatics
Biological Evolution
Biomedical and Life Sciences
Breakpoints
computer software
Evolutionary Biology
genes
Genome
Genomes
Genomics
Human Genetics
Hypotheses
Internet
Life Sciences
Microbial Genetics and Genomics
Plant Genetics and Genomics
Software
Synteny
User interface
Visualization
Web Browser
world wide web
ISSN:1474-760X, 1474-7596, 1474-760X
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Popis
Shrnutí:We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-023-02914-z