Viral variant calling with Galaxy

The analysis of a viral genome and its variants has unique challenges, most notably the inability to culture the virus outside of the host organism. Furthermore, many viruses have a high mutational rate which, coupled with the culturing restrictions, make determining viral variants more of a heterogeneous population exercise.

In this online workshop we focus on the tools and workflows available for variant calling in viruses in Galaxy Australia. During the workshop you will get hands-on experience using BWA-MEM for alignment, lofreq for variant calling and SnpEff for annotating variant effects. The workshop makes use of COVID-19 variant calling data however the tools and workflows are equally applicable to other viruses and biological questions.

Access to all of the tools covered in this workshop is via Galaxy Australia, an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience.

You may also be interested in our workshops on variant calling in polyploid organisms (e.g animals, plants, humans) and bacteria. See our events listings for more information.

Date/time: 1-5pm AEST, Wednesday 26 May 2021

Lead Trainers: Dr Gareth Price and Dr Igor Makunin, QCIF Bioinformatics.

Learning outcomes

The materials to be covered in the workshop are freely available via the Galaxy Training Network.

By the end of the workshop you should be able to:

• Download and import reference genome data
• Align reads using BWA-MEM
• Call variants using lofreq
• Annotate variant effects with SnpEff

The workshop will NOT provide an introduction to the basics of Galaxy or the use of Galaxy for sequencing analysis (e.g. quality control and mapping). If you would like to learn about these topics there are several tutorials available via the Galaxy Training Network.

Who the workshop is for

This workshop is for Australian researchers who have or will work on variant calling in viruses as part of their projects.

To get the most out of the workshops you must be familiar with the concepts of variant calling and have some experience with the basics of using Galaxy Australia such as setting up a history, uploading data and running tools. No programming experience is required.

You will be required to watch an introductory webinar (either live or recorded) that will provide an overview of Galaxy Australia and introduce key functionalities of the service. If you are new to Galaxy we recommend that you work through the following tutorials in advance: A short introduction to Galaxy and Galaxy 101 for Everyone.

How to apply

This workshop is free but participation is subject to application with selection. Applications close at 5pm AEST Wednesday 12 May 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 14 May 2021. Successful applicants will be provided with a Zoom meeting link closer to the date.

This workshop is presented by the Australian BioCommons and Queensland Cyber Infrastructure Foundation (QCIF) with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative and Galaxy Australia.

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: Colourised transmission electron micrograph shows H1N1 influenza virus particles. National Institutes of Health (NIH). Wikimedia commons.