Educators:
Jochen Blom, Oliver Schwengers, Oliver Rupp (BiGi)

Date:
11.12.2023 – 12.12.2023

Location:
Justus Liebig University Giessen, Heinrich-Buff-Ring 58, Room 0024a

Contents:
Topic of this two-day-workshop will be sequence data analysis of microbial genomes. This will include quality control, assembly, genome annotation and comparative genomics using standard bioinformatics software tools (FastQC, SPAdes, Unicycler) and the de.NBI software tools like the annotation tool Bakta and the comparative genomics platform EDGAR. Furthermore, we will present our new standardized bacterial sequence information repository BakRep, and we will give a short introduction on the quick and easy submission of validated genome data to INSDC databases.

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
Furthermore, we will present our new large-scale bacterial genome repository BakRep. We will explain the various contents of this repository and showcase how to use this for interactive bacterial genome screenings followed by large-scale batch downloads for downstream analyses.

Finally, there will be a short introduction on how to validate and submit genome sequences to the ENA database by using the Webin Command line tool.

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)
Comparison of functional classifications (KEGG, COG, GO)
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.

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

Prerequisites:

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

Tools:
FastQC, SPAdes, Unicycler, Bakta, BakRep, Webin-CLI, EDGAR