Genome assembly with Galaxy (and command line)
This 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.
Biologists and bioinformaticians interested in genome sequencing and the assembly process, particularly for bacteria. No prior bioinformatics knowledge is required.
- 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
- 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