Educators:
Jochen Blom, Oliver Schwengers (BiGi)

Date:
02.09.2020

Location:
Online Training Room

Contents:
Topic of this one-day-workshop will be sequence data analysis of microbial genomes. This will include quality control, assembly, genome annotation and comparative genomics using the de.NBI software tools ASA3P and EDGAR.

The one-day-course will be separated in two sessions, one in the morning and one in the afternoon.
In the morning session, the basic principles of regional and functional annotation will be introduced, and available tools and algorithms for the different annotation steps will be explained. The ASA3P platform for high-throughput parallel genome annotation and its capabilities in antibiotic resistance and virulence factor detection will be presented in detail.
• The basic principles of regional and functional annotation
• Genome annotation pipelines for single and multiple genomes
• High throughput genome annotation using ASA3P

In the afternoon session, the EDGAR platform for comparative genomics will be introduced. One main topic will be its use for phylogenetic analyses based on genome similarity indices and the complete core genome of organisms. All features of EDGAR will be introduced in detail.
• Genomic subset calculations (core-genome, pan-genome, singleton genes)
• Core-genome-based phylogenetic analyses
• Core genome based phylogeny
◦ ANI, AAI, POCP
• Statistical analyses (core/pan/singleton development plots)
• The public EDGAR database

After the EDGAR presentation, there will be time for custom data analysis consulting. Participants with own data which needs to be analyzed are encouraged to discuss their projects with the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi).

In both sessions, the program includes extensive hands-on training to allow participants to become familiar with the presented software.

Learning goals:
Principles of computational sequence analysis, hands-on experience with de.NBI software services

Prerequisites:

Keywords:
Sequence data analysis, genomics, annotation, comparative genomics, phylogenetic analysis

Tools:
ASA3P, EDGAR