7th de.NBI Genomics training course (Dec 12th & 13th 2022)

The two-day-course will be separated in three sessions, session I in the afternoon of day one and session II and III in the morning and afternoon of day two, respectively.

Session I will cover the field of genome assembly, the reconstruction of the genomic DNA sequence from short sequencing reads.
This session gives an introduction to the main concepts, algorithms and tools for de novo genome assemblies. The course also focuses on the quality assessment of the sequencing data and introduces quality metrics to compare different assembly results. The participants will gain practical experiences in a hands-on session using the Galaxy platform.

• QA/QC of raw sequencing data
• Assembly concepts and algorithms
• QA/QC of assembled genomes
• Computing assemblies with Galaxy

In session II, 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 de.NBI software tool Bakta for high-quality but nevertheless fast bacterial genome annotation will be presented in detail.

• The basic principles of regional and functional annotations
• Bacterial genome annotation with Bakta
• Hands-on examples via web and command-line interfaces

In session III, 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 subsets (core-genome, pan-genome, singleton genes)
• Core-genome-based phylogenetic analyses
• 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 all sessions, the program includes extensive hands-on training to allow participants to become familiar with the presented software

Agenda:

Monday, 12.12.2022, afternoon session: Genome assembly

12:00 – 13:00
Arrival of participants

13:00 – 13:15
Welcome & introduction

13:15 – 14:30
Introduction to genome assembly (Oliver Rupp)

14:30 – 15:00
Short break

15:00 – 16:30
Hands on: bacterial genome assembly with Galaxy (Oliver Rupp)

Tuesday, 13.12.2022, morning session: Genome annotation

09:00 – 10:15
Introduction to Genome annotation (Oliver Schwengers)

10:15 – 10:30
Short break

10:30 – 12:00
Introduction to ASA3P (Oliver Schwengers)

12:00 – 13:00
Lunch break

Tuesday, 13.12.2022, afternoon session: Comparative Genomics

13:00 – 14:30
Introduction to the EDGAR platform (Jochen Blom)

14:30 – 14:45
Short break

14:45 – 16:00
EDGAR demo and hands-on (Jochen Blom)

Location

This workshop is an in-person event and participation is free of charge; the workshop will take place at the old chemistry building of the Justus Liebig University, Heinrich-Buff-Ring 58, 35392 Giessen, in rooms 0024a (workshop) and 0001 (coffee breaks and lunch). Once you enter the building, the way to the workshop will be sign-posted.

Contact & Registration:
Via mail to genomics_course@computational.bio
Please indicate dietary requirements (vegetarian, allergies, ..), if applicable.