2025 Semester 1 Workshop 1 (S1W1) - HPC and Bioinformatics (variant calling & metagenomics)

Overview

This series of hands-on workshops is designed for HDR students and Staff at QUT interested in running reproducible, scalable, and portable Nextflow pipelines, with downstream Differential Expression and Functional Annotation analyses for RNAseq or small RNAseq datasets. These workshops are designed for people with no command line/HPC experience & no/little bioinformatics skills. This is an introductory course delivered over 7 workshops at Gardens Point.

Benefits

Researchers enrolling in the entire series of workshops will learn how to use and run bioinformatics pipelines using basic command line skills, NextFlow pipelines and R scripts, while those enrolling in just the first 2 workshops will learn how to log on to QUT’s HPC to copy files, edit scripts and submit jobs.

Who should attend the training

This training is suitable for new users of the HPC or those with little-to-no experience in analysing RNAseq datasets. These sessions are introductory only.

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.

Workshops Sessions:

Sessions	Date*	Room	Registration
Intro to Nextflow	9:30 am-12pm Mon 10 Mar → Rescheduled to Mon 17 March due to Ex-TC Aldred	GP-S-502	N/A
Variant calling analysis and annotation using the Nextflow nf-core/sarek pipeline	9:30am-12pm Mon 17 March	GP-S-502	Book here
Metagenomics analysis using the Nextflow nf-core/ampliseq pipeline	9:30am-12pm Mon 24 March	GP-S-502	Book here
Downstream metagenomics analysis using R	9:30am-12pm Mon 31 March	GP-S-502	Book here

More information

More information on the content of each workshop can be found under Training Resources.

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