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Refining Genome Annotations with Apollo

Contributors

Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet

Questions

Objectives

last_modification Last modification: Jun 4, 2021

Genome annotation

.image-50[JBrowse screenshot showing several genes aligned along a genome]

Speaker Notes


Automatic annotations are not perfect

.pull-left[

.pull-right[.image-40[Apollo screenshot showing how RNASeq reads align mostly within some exons limits, but not perfectly]]

Speaker Notes


Manual curation refines genome annotations

.pull-left[.image-90[Schema showing how automated annotation, experimental evidences (cDNAs, HMM domain searches, RNASeq, similarity with other species), and human analysis are used by Apollo to manually curate an annotation]]

.pull-right[.image-40[Apollo screenshot showing how RNASeq reads align mostly within some exons limits, but not perfectly]]

Speaker Notes


Apollo

“Google Docs for Genome Annotation”

.image-50[Screenshot of Apollo in Galaxy, apollo takes up most of the space in the center iframe with the history shown on the right.]

Collaborative web application to edit annotation

Both structural and functional annotation

Based on JBrowse: JBrowse is for visualising only, Apollo allows to edit

Speaker Notes


Apollo

.pull-left[.image-90[Animation showing how the limit of an exon can be changed within Apollo by a simple drag-and-drop]] .pull-right[.image-90[Screenshot of the Apollo form allowing to edit functional annotation]]

Speaker Notes


Apollo

Multi user environment: users can login, and make/see changes in realtime

Full history of changes, reverting is possible

Screenshot of the history panel, with a list of actions and possibility to revert

Speaker Notes


Apollo in Galaxy

Integrate Apollo in your whole analysis project in Galaxy

  1. Run assembly
  2. Align evidences along the genome (RNASeq, CDS, proteins)
  3. Run automatic annotation pipeline
  4. Create a JBrowse instance
  5. Load the JBrowse instance into Apollo
  6. Use Apollo to manually curate annotation with collaborators
  7. Export back the curated annotation into Galaxy
  8. Continue analysing in Galaxy

Available on https://usegalaxy.eu

Speaker Notes


Apollo in Galaxy: collaborating

Invite any other Galaxy user to your curation project

Screenshot of the dialog allowing to share the access to other users

Speaker Notes


hands_on Hands on!

Time to follow the Apollo tutorial!

Speaker Notes


Key Points

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.