WEBINAR: Where to go when your bioinformatics outgrows your compute
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute...
Keywords: Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WEBINAR: Where to go when your bioinformatics outgrows your compute
https://zenodo.org/records/5240578
https://dresa.org.au/materials/webinar-where-to-go-when-your-bioinformatics-outgrows-your-compute-7a5a0ff8-8f4f-4fd0-af20-a88d515a6554
This record includes training materials associated with the Australian BioCommons webinar ‘Where to go when your bioinformatics outgrows your compute’. This webinar took place on 19 August 2021.
Bioinformatics analyses are often complex, requiring multiple software tools and specialised compute resources. “I don’t know what compute resources I will need”, “My analysis won’t run and I don’t know why” and "Just getting it to work" are common pain points for researchers. In this webinar, you will learn how to understand the compute requirements for your bioinformatics workflows. You will also hear about ways of accessing compute that suits your needs as an Australian researcher, including Galaxy Australia, cloud and high-performance computing services offered by the Australian Research Data Commons, the National Compute Infrastructure (NCI) and Pawsey. We also describe bioinformatics and computing support services available to Australian researchers.
This webinar was jointly organised with the Sydney Informatics Hub at the University of Sydney.
Materials are shared under a Creative Commons Attribution 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Where to go when your bioinformatics outgrows your compute - slides (PDF and PPTX): Slides presented during the webinar
Australian research computing resources cheat sheet (PDF): A list of resources and useful links mentioned during the webinar.
Materials shared elsewhere:
A recording of the webinar is available on the Australian BioCommons YouTube Channel:
https://youtu.be/hNTbngSc-W0
Melissa Burke (melissa@biocommons.org.au)
Samaha, Georgina (orcid: 0000-0003-0419-1476)
Chew, Tracy (orcid: 0000-0001-9529-7705)
Sadsad, Rosemarie (orcid: 0000-0003-2488-953X)
Coddington, Paul (orcid: 0000-0003-1336-9686)
Gladman, Simon (orcid: 0000-0002-6100-4385)
Edberg, Roger
Shaikh, Javed
Cytowski, Maciej (orcid: 0000-0002-0007-0979)
Computational Biology, Bioinformatics, High performance computing, HPC, Galaxy Australia, Nectar Research Cloud, Pawsey Supercomputing Centre, NCI, NCMAS, Cloud computing
WORKSHOP: Variant calling in humans, animals and plants with Galaxy
This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.
Variant calling in polyploid organisms, including humans, plants and animals, can help determine single...
Keywords: Variant calling, Genetic Variation Analysis, SNP annotation
WORKSHOP: Variant calling in humans, animals and plants with Galaxy
https://zenodo.org/records/5076668
https://dresa.org.au/materials/workshop-variant-calling-in-humans-animals-and-plants-with-galaxy-767f1816-1c06-478c-adf4-90b3b2d32a9c
This record includes training materials associated with the Australian BioCommons workshop ‘Variant calling in humans, animals and plants with Galaxy’. This workshop took place on 25 May 2021.
Variant calling in polyploid organisms, including humans, plants and animals, can help determine single or multi-variant contributors to a phenotype. Further, sexual reproduction (as compared to asexual) combines variants in a novel manner; this can be used to determine previously unknown variant - phenotype combinations but also to track lineage and lineage associated traits (GWAS studies), that all rely on highly accurate variant calling. The ability to confidently call variants in polyploid organisms is highly dependent on the balance between the frequency of variant observations against the background of non-variant observations, and even further compounded when one considers multi-variant positions within the genome. These are some of the challenges that will be explored in the workshop.
In this online workshop we focused on the tools and workflows available for variant calling in polyploid organisms in Galaxy Australia. The workshop provided opportunities for hands-on experience using Freebayes for variant calling and SnpEff and GEMINI for variant annotation. The workshop made use of data from a case study on diagnosing a genetic disease however the tools and workflows are equally applicable to other polyploid organisms and biological questions.
Access to all of the tools covered in this workshop was 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.
The materials are shared under a Creative Commons 4.0 International agreement unless otherwise specified and were current at the time of the event.
Files and materials included in this record:
Event metadata (PDF): Information about the event including, description, event URL, learning objectives, prerequisites, technical requirements etc.
Index of training materials (PDF): List and description of all materials associated with this event including the name, format, location and a brief description of each file.
Schedule (PDF): schedule for the workshop
Variant calling - humans, animals, plants - slides (PPTX and PDF): slides used in the workshop
Materials shared elsewhere:
The tutorial used in this workshop is available via the Galaxy Training Network.
Wolfgang Maier, Bérénice Batut, Torsten Houwaart, Anika Erxleben, Björn Grüning, 2021 Exome sequencing data analysis for diagnosing a genetic disease (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html Online; accessed 25 May 2021
Melissa Burke (melissa@biocommons.org.au)
Price, Gareth (orcid: 0000-0003-2439-8650)
Variant calling, Genetic Variation Analysis, SNP annotation