Bacterial variant calling with Galaxy

Bacteria evolve rapidly, acquiring and purging DNA changes in response to their changing environments. Many bacteria can be cultured, allowing researchers to study DNA variants from a single organism source, unlike variant analysis in polyploids. Comparison of variants between single organisms gives insight not only into their individual characteristics (such as antimicrobial resistance) but at a population level allows for phylogenetic mapping to determine the relatedness between samples.

In this online workshop we focus on the tools and workflows available for variant calling in bacteria in Galaxy Australia. During the workshop you will get hands-on experience using Snippy for genetic variation detection and annotation, and JBrowse to visualise variants. The workshop makes use of data from a case study on antimicrobial resistance in Mycobacterium tuberculosis however the tools and workflows are equally applicable to other bacteria 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 viruses. See our events listings for more information on other workshops and events.

Date/time: 1-5pm AEST, Thursday 27 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:

• Detect genetic variation in microbial genomes using Snippy
• Visualise variants in a genome browser (JBrowse)
• Use annotations to infer changes to phenotype

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 bacteria 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: Escherichia coli. Pixabay.