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JBrowse



last_modification Updated:   purlPURL: gxy.io/GTN:S00102

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Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

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JBrowse for Genomics Visualisation

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What is JBrowse

  • Interactive genome browser
  • HTML5 / Javascript
  • Process data + copy directory to a webserver
  • Can be deployed to apache/nginx, S3 buckets, etc.
  • Many plugins available for
    • Themes
    • Datatype support (mafviewer, agp_parser)
    • Third party data integration (GA4GH, MyVariantViewer)
    • Visualisations (GC Content track, Sashimi for RNAseq)
    • More

jbrowse screenshot

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JBrowse in Galaxy

  • Tool that produces a JBrowse instance (client side code + processed data)
  • Workflow compatible
  • Covers most of the possibilities of JBrowse
  • Supports many Galaxy datatypes:
    • GFF3 / GBK /BED
    • BAM (SAM)
    • (big)Wig
    • Blast XML
    • VCF
    • REST/SPARQL endpoints
  • Complex JBrowse made easy (Thanks Galaxy!)
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Built in Provenance Tracking

  • "ComboTrackSelector" supports attaching metadata to tracks + filtering
  • We attached Galaxy metadata
    • Dataset Creator
    • Dataset Job Parameters
    • Tool + Version
    • Date
  • Can "build on top of" existing JBrowses, adding more data. Complete history tracked.

provenance tracking

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Why is this Necessary?

  • JBrowse allows you to present Galaxy analysis workflows in a single visualisation
  • Researchers generally understand genome browsers
  • When annotation, not just visualisation, is needed, the JBrowse instances can be sent to Apollo
  • Apollo allows for collaborative genome annotation and curation
  • Check out the Apollo tutorials for more details: prokaryotes - eukaryotes
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Why do you need this?

  • You are running genome annotation or genomic data analysis workflows
  • Researchers need more visual outputs than tables of data
  • Datasets can be more valuable visualised together, rather than as separate lines in a report
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Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s) orcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemann
Reviewers Björn Grüning avatarAnthony Bretaudeau avatarHelena Rasche avatarSaskia Hiltemann avatar
Galaxy Training Network

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

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JBrowse for Genomics Visualisation

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