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 will make 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 join our webinar on 29 September 2021.
Trainers
Anthony Bretaudeau (French National Institute for Agriculture, Food, and Environment), Helena Rasche (Erasmus Medical Center, The Netherlands), Dr Sarah Williams (QCIF), Dr Tiffanie Nelson (Australian BioCommons)
Date/Time
3-6pm AEDT/ 2-5pm AEST/ 2:30-5:30pm ACDT / 12-3pm AWST, Wednesday 17 Nov 2021
Learning outcomes
By the end of the workshop you should be able to:
Upload data to Apollo
Visualise your genome and associated automated annotations
Manually annotate genomes after automated annotations have been performed
Evaluate and visualise annotated genomic features
Use Apollo to collaborate on genome annotation
This workshop is based on training materials developed for the Galaxy Training Network and the Apollo User Guide.
Who the workshop is for
This workshop is for Australian researchers who have or will work on genome annotation and manual curation/editing as part of their projects.
You should be familiar with the concepts of genome annotation and have, or soon have, genome annotation files that require manual annotation and curation.
You do not need access to a personal or institutional instance of Apollo for this workshop. Access to a training instance of the Australian Apollo Service will be provided.
How to apply
This workshop is free but participation is subject to application with selection. Applications close at 11:59pm AEDT, Thursday 4 November 2021.
You must be associated with an Australian organisation and provide an appropriate organisational email address for your application to be considered.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 12 November 2021. Successful applicants will be provided with a Zoom meeting link closer to the date.
Applications have closed
The training materials from this workshop are available via Zenodo.
This workshop is 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.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons
Cover image: Apollo logo