This 1.5-day workshop will include a short introduction to next-generation sequencing theory and an introduction to Galaxy. The hands-on component of the workshop will cover the concepts of de novo assembly and initial annotation of a genome from short-read NGS data.
Variant detection using Galaxy (15-16 May 2018)
Tue, 15/05/2018 - 09:00 to Wed, 16/05/2018 - 12:30
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.
- 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
- 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