Bacterial Genome Assembly and Annotation in Galaxy

BeginnersNew

The workshop will cover the basics of de novo genome assembly using a small genome example. This includes project planning steps, selecting fragment sizes, initial assembly of reads into fully covered contigs, and then assembling those contigs into larger scaffolds that may include gaps. The end result will be a set of contigs and scaffolds with sufficient average length to perform further analysis on, including genome annotation (link to that nomination). This workshop will use tools and methods targeted at small genomes. The basics of assembly and scaffolding presented here will be useful for building larger genomes, but the specific tools and much of the project planning will be different.

This workshop will also introduce genome annotation in the context of small genomes. We’ll begin with genome annotation concepts, and then introduce resources and tools for automatically annotating small genomes. The workshop will finish with a review of options for further automatic and manual tuning of the annotation, and for maintaining it as new assemblies or information becomes available.

This session will include an introduction to the Galaxy platform.

This event is co-organized with EMBL-ABR and the Genomics Virtual Lab. Course materials can be found here.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

• Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
• Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
• Further details regarding eligibility criteria are available here

Number of sessions: 1

After this course you should have an understanding of:

• how bacterial genome assembly works and how to run such analysis
• how genome annotation works and be able to annotate a small genome

During this course you will learn about:

• Introduction to Galaxy
• Brief introduction to next generation sequencing data
• Genome assembly and its parameters
• Automatic genome annotation pipeline

Presentations, demonstrations and practicals

• Free for University of Cambridge students
• £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 100/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1

A number of times per year

• Introduction to high-throughput sequencing data analysis
• Analysis of mapped NGS data with SeqMonk (ONLINE LIVE TRAINING)
• Introduction to RNA-seq and ChIP-seq data analysis
• Analysis of RNA-seq data with Bioconductor
• Analysis of small RNA-seq data
• An Introduction to Solving Biological Problems with R