This collection presents step-by-step guides that support the reuse of Galaxy workflows created in collaboration with the Bioplatforms Australia Threatened Species Initiative (TSI). There are guides for genome assembly and quality control, RAD-seq analysis with Stacks, and more!
Other guides are available at the BioCommons How-to Hub, the central location for all guides and associated documents that have been prepared by community members who gather around BioCommons activities.
Genome assembly
It is important to assess the quality of a genome assembly, and in the first instance, this quality control (QC) can be achieved using the workflow described here
This guide describes the steps required to assemble your genome on the Galaxy Australia platform using multiple workflows
This guide describes the steps required to scaffold your genome on the Galaxy Australia platform using HiC data
Genome annotation
Population genomics
This guide describes the steps required to run multiple Stacks workflows on Galaxy Australia to analyse RADseq data.
Contributors
These guides would not be possible without the following contributors.
Anna Syme
Bert Droesbeke
Gareth Price
QCIF Bioinformatics, University of Queensland
Jo Day
Taronga Conservation Society Australia
Editor
Johan Gustafsson
Australian BioCommons, University of Melbourne
Kate Farquharson
University of Sydney (School of Life and Environmental Sciences) and ARC Centre of Excellence for Innovations in Peptide and Protein Science
Luke Silver
School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
Mike Thang
Simon Tang
Tiff Nelson
Australian BioCommons, Griffith University
Tom Harrop
Wai Cheng (Mike) Thang
QCIF Bioinformatics, University of Queensland
Acknowledgements
This work is supported by the Australian BioCommons via funding from Bioplatforms Australiaand the Queensland Government RICF programme. Bioplatforms Australia is funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
These guides were first developed as part of the Australian BioCommons BYOD Expansion Project, which was is funded through NCRIS investments from Bioplatforms Australia and the Australian Research Data Commons ([http://doi.org/10.47486/PL105]) that were matched by co-investments from AARNet, Melbourne Bioinformatics, NCI, Pawsey, QCIF via the Queensland Government RICF fund, The University of Sydney, AGRF, Griffith University and Monash University.
This repository makes use of the ELIXIR toolkit theme:
