last_modification Last modification: Jun 4, 2021
JBrowse for Genomics Visualisation
What is JBrowse
- Interactive genome browser
- Process data + copy directory to a webserver
- Can be deployed to apache/nginx, S3 buckets, etc.
- Many plugins available for
- Datatype support (mafviewer, agp_parser)
- Third party data integration (GA4GH, MyVariantViewer)
- Visualisations (GC Content track, Sashimi for RNAseq)
- More ]
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)
- Blast XML
- REST/SPARQL endpoints
- Complex JBrowse made easy (Thanks Galaxy!)
Built in Provenance Tracking
- “ComboTrackSelector” supports attaching metadata to tracks + filtering
- We attached Galaxy metadata
- Dataset Creator
- Dataset Job Parameters
- Tool + Version
- 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 tutorial for more details.
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