Variant detection using Galaxy
This workshop will cover the concepts of detection 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 workshop will all be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools.
Biologists and other life scientists planning to work with next-generation sequencing data for small variant detection. Participants must bring their own laptops with wireless network capability.
- 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
- Access and use of the Galaxy bioinformatics analysis platform
- Quality control and filtering of next-generation sequencing data
- Next-generation sequencing read mapping
- Visualisation of mapped reads with the Integrative Genomics Viewer
- Use of and comparison of software applications to call genomic variants
- Filtering and screening protocols to generate lists of high-confidence SNPs
- Initial annotation of the predicted biological impact of identified variants