This hands-on workshop will introduce the building blocks of the Python scripting environment. Participants will learn about basic programming concepts including simple and complex data types, conditionals and looping that are applicable to Python and other languages.
Variant detection using Galaxy (02-Mar-2017)
This workshop has been postponed to April 2017.
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.
- 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