2024 - Semester One: Hands-on variant calling and metagenomics analyses using QUT's HPC and Nextflow
- Roberto Barrero Gumiel
- Paul Whatmore (Deactivated)
This hands-on workshop is designed for HDRs and Staff at QUT with no command line or bioinformatics experience and for those with Bioinformatics skills interested in running reproducible, scalable, and portable Nextflow pipelines for variant calling and metagenomics analyses. The workshops will allow participants to use and run bioinformatics pipelines using basic command line skills and Jupyter Notebooks.
Date: 7th May - 4th June 2024
Venue: GP S506
Short URL link:
https://eresearchqut.atlassian.net/l/cp/WU1ru1e0
HPC Account
The first session is all about using the HPC. You will need a HPC account to take part in the session. If you do not have one, please request one here.
Brief Survey
Fill a short survey by Monday 6 May 2024. Alternatively, scan the following QR code to access the survey:
Workshop Sessions
Five workshop sessions will introduce participants to using QUT’s HPC, running bioinformatics pipelines for variant calling and metagenomics analyses. Find below information on individual sessions. In case you have not yet registered for all sessions of interest, feel free to register using the direct UniHub links below:
Session | Description | Date | Time | Location | UniHub |
1 | Bioinformatics - Introduction to the HPC and basic Unix commands | 7 May | 9.00 am – 12.00 noon | GP-S-506 | N/A |
2 | Bioinformatics - Variant calling data analysis using Illumina datasets | 14 May | 9.00 am – 12.00 noon | GP-S-506 | |
3 | Bioinformatics - Variant calling using Oxford Nanopore data | 21 May | 9.00 am – 12.00 noon | GP-S-506 | |
4 | Bioinformatics - Introduction to metagenomics using Illumina data | 28 May | 9.00 am – 12.00 noon | GP-S-506 | |
5 | Bioinformatics - Metagenomics using Nanopore and downstream analysis in R | 4 June | 9.00 am – 12.00 noon | GP-S-506 |
Hands-on training materials
Session 2 - Variant calling analysis
Session 3 - Variant analysis using Nanopore data
Session 4: Metagenomics (amplicon sequencing analysis)
Session 5: Analysis of amplicon sequencing results in R
Final Survey
We are keen to get your feedback to help us improve future training workshops. Please take 5-10 min to respond to the final survey (it is anonymous). Alternatively, scan the QR below to access the survey.
