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JBrowse 2: a modular genome browser with views of synteny and structural variation.
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.
Afiliación
  • Diesh C; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Stevens GJ; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Xie P; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • De Jesus Martinez T; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Hershberg EA; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Leung A; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Guo E; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Dider S; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Zhang J; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Bridge C; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Hogue G; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Duncan A; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Morgan M; Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University, Corvallis, OR, 97331, USA.
  • Flores T; Center for Applied Systems and Software, 224 Milne Computer Center, 1800 SW Campus Way, Oregon State University, Corvallis, OR, 97331, USA.
  • Bimber BN; Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
  • Haw R; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Cain S; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Buels RM; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA.
  • Stein LD; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada.
  • Holmes IH; Department of Bioengineering, Stanley Hall, University of California, Berkeley, CA, 94720, USA. ihh@berkeley.edu.
Genome Biol ; 24(1): 74, 2023 04 17.
Article en En | MEDLINE | ID: mdl-37069644
ABSTRACT
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Genómica Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Genómica Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos