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.
Genome assembly using Galaxy (2-3 Aug 2017)
Wed, 02/08/2017 - 09:00 to Thu, 03/08/2017 - 12:30
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. You will be introduced to the widely-used de novo assembly pipeline, including quality checking, trimming, concepts of filtering, concepts of annotation and use a selection of tools to identify genomic features of interest.
The workshop will all be based in Genomics Virtual Lab, a platform that provides access to already installed bioinformatics tools.
- Tools and workflows of de novo genome assembly
- Online resources for bacterial genome annotation
- Identifying genomic features of interest, including insertions, deletions and duplications
- Use of the Galaxy platform for genome analysis
- Perform QC evaluation and filtering on next-generation sequencing data
- Carry out a bacterial genome assembly using the Galaxy interface
- Generate preliminary annotation data for a bacterial genome sequence
- Use comparative genomics approaches to identify large genomic insertions and deletions