This bioinformatics workshop will cover the concepts of detecting small variants, including SNPs and small indels, from next-generation sequencing data. You will use and compare a number of popular variant detection tools, visualise variants using a genome browser, and annotate SNPs for predicted biological effects.
The training course will all be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools.
Recommended participants
Biologists and bioinformaticians planning to work with next-generation sequencing data for small variant detection. No prior bioinformatics knowledge is required.
What will I learn?
During this course you will learn about:
- The tools and workflows of SNP and indel detection
- Quality filtering and other techniques for improving SNP prediction accuracy
- Comparison of variant detection software
- The use of the Galaxy platform for variant detection analysis
After this course you should be able to:
- Perform QC evaluation and filtering on next-generation sequencing data
- Select and use relevant variant detection software and apply appropriate quality filters to screen variants
- View variant and sequence data using the Integrative Genomics Viewer (IGV)
- Carry out preliminary functional annotation of predicted variants
Your trainer
Dr Mark Crowe joined QFAB as Training and Outreach Manager in late 2012. Mark is a certified trainer with over fifteen years experience in genomics and bioinformatics. His experience has included providing bioinformatics support for a pan-European microarray development project, running Australia’s largest next-generation sequencing service facility, and research and operational management in a commercial agricultural genomics company.
Contact Mark Crowe [email protected] / 07 3346 2095 for further information about QFAB training.
