WORKSHOP: Refining genome annotations with Apollo

This record includes training materials associated with the Australian BioCommons  workshop ‘Refining genome annotations with Apollo’. This workshop took place on 17 November 2021.

Workshop description 

Genome annotation is crucial to defining the function of genomic sequences. This process typically involves a round of automated annotation followed by manual curation. Manual curation allows you to visualise your annotations so you can understand what your organism looks like, and then to manually refine these annotations along with any additional data you might have. This process is typically performed collaboratively as part of a team effort.

Apollo is a popular tool for facilitating real-time collaborative, manual curation and genome annotation editing. In this workshop we will learn how to use Apollo to refine genome annotations using example data from an E. coli strain. We’ll focus on the basics like getting data into Apollo, viewing evidence tracks, editing and adding structural and functional annotation, visualising the results and collaborating on genome annotations.

This workshop made use of a training instance of  the new Australian Apollo Service. This service enables Australian-based research groups and consortia to access Apollo and host genome assembly and supporting evidence files for free. This service has been made possible by The Australian BioCommons and partners at QCIF and Pawsey. To learn more about the Australian Apollo Service you can watch the Australian Apollo Launch Webinar.

This workshop was presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) .

The Australian Apollo Service is operated by QCIF and underpinned by computational resources provided by the Pawsey Supercomputing Research Centre and receives NCRIS funding through Bioplatforms Australia and the Australian Research Data Commons as well as Queensland Government RICF funding.

The training materials presented in this workshop were developed by Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet for the Galaxy Training Network. Helena and Anthony are part of the Gallantries project which is supported by Erasmus+ Programme of the European Union.

Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.

Files and materials included in this record:

• Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.

• Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.

• Schedule (PDF): A breakdown of the topics and timings for the workshop

• 2021 Apollo Training Intro (PPTX and PDF): Slides used to introduce the Australian Apollo Service

• Augustus.gff3 (gff3): E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.

• Blastp_vs_swissprot.gff3: E.coli derived data file used in the tutorial. Data was obtained from the Galaxy Training Network and pre-processed using Galaxy Australia.

Materials shared elsewhere:

This workshop is based on the tutorial ‘Refining genome annotations with Apollo’ which was developed for the Galaxy Training Network.

Anthony Bretaudeau, Helena Rasche, Nathan Dunn, Mateo Boudet, Erasmus+ Programme, 2021 Refining Genome Annotations with Apollo (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/apollo/tutorial.html Online; accessed Wed Dec 15 2021

See also:

Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012