JBrowse

Contributors

Helena Rasche Saskia Hiltemann

JBrowse for Genomics Visualisation

What is JBrowse

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• 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 ]

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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!)

JBrowse2: New version and new possibility

• Hi-C data visualization for 3D representation of chromosomal interactions
• Circular view, ideal for analyzing bacterial genomes or plasmids
• Added dotplots in tracks
• New formats (e.g., CRAM)
• And much more …

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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.

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

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

Thank you!