JBrowse

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# JBrowse

<div class="contributors-line">
		Authors: 
<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/hexylena?s=27" alt="Avatar">Helena Rasche</a>

<a href="/training-material/hall-of-fame/shiltemann/" class="contributor-badge contributor-shiltemann"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/shiltemann?s=27" alt="Avatar">Saskia Hiltemann</a>

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<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Aug 22, 2022</div>

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## Requirements

Before diving into this slide deck, we recommend you to have a look at:

- [Introduction to Galaxy Analyses](/training-material/topics/introduction)

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# JBrowse for Genomics Visualisation

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### What is JBrowse

.pull-left[
- Interactive genome browser
- HTML5 / Javascript
- Process data + copy directory to a webserver
- Can be deployed to apache/nginx, S3 buckets, etc.
- Many [plugins](https://gmod.github.io/jbrowse-registry/) available for
  - Themes
  - Datatype support (mafviewer, agp_parser)
  - Third party data integration (GA4GH, MyVariantViewer)
  - Visualisations (GC Content track, Sashimi for RNAseq)
  - More
]

.pull-right[
![jbrowse screenshot](../../images/jbrowse/sequencing.png)
]

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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](../../images/jbrowse/provenance.png)

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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](/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html) - [eukaryotes](/training-material/topics/genome-annotation/tutorials/apollo-euk/tutorial.html)

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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](https://training.galaxyproject.org) and all the contributors!

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<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
This material is licensed under the Creative Commons Attribution 4.0 International License</a>.