Genome Assembly Using Galaxy

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 be based in Galaxy, a platform that provides a simple and user-friendly interface to bioinformatics tools.

Recommended Participants

Biologists and bioinformaticians interested in genome sequencing and the assembly process, particularly for bacteria. No prior bioinformatics knowledge is required.

Learning Objectives

• 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

Syllabus

• 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