Researcher Training Day for Life Scientists_ Rad-seq with Stacks in Galaxy

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EMBL Australia Bioinformatics Resource (EMBL-ABR) is a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia.
EMBL-ABR aims to:

increase Australia’s capacity to collect, integrate, analyse, exploit, share and archive the large heterogeneous data sets now part of modern life sciences research
contribute to the development of and provide training in data, tools and platforms to enable Australia’s life science researchers to undertake research in the age of big data
showcase Australian research and datasets at an international level
enable engagement in international programs that create, deploy and develop best practice approaches to data management, software tools and methods, computational platforms and bioinformatics services.

EMBL-ABR is structured as a hub/nodes model, with the Hub located at Melbourne Bioinformatics (formerly VLSCI), University of Melbourne. EMBL-ABR is also currently exploring engagement with the European infrastructure for biological information, ELIXIR, and other relevant international efforts.

One of EMBL-ABR Key areas is TRAINING, and as such we are involved in diverse projects relevant for bioinformatics training in Australia, with a current focus on Open Science and Bioinformatics.

Researcher Training Day for Life Scientists_ Rad-seq with Stacks in Galaxy

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This session demonstrated how to use Stacks tools wrapped in Galaxy to process your RAD-seq (Restriction-site Associated DNA sequencing) data for population genomics. We started with raw sequencing reads and take them through quality-control, and de novo assembly steps. We then demonstrated the use of Stacks tools in Galaxy to call variants, build a variant catalogue and output filtered variant calls for downstream analysis.

We also touched on some of the options in molecular approach to RAD-seq library design and explained the important considerations for different research questions and species of interest.

This session included an introduction to the Galaxy platform.

Licence: Other (Attribution)

Keywords: bioinformatics

Target audience: Biologists

Authors: Vicky Schneider

Contributors: Pip Griffin, Sonika Tyagi

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