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

Date
24.06.2026-26.06.2026

Location
Justus Liebig University Giessen, Seltersweg 85, Bioinformatics Lab

Contents
Topic of this three-day-workshop will be whole-genome sequence data analysis of microbial genomes. This will include quality control, assembly, genome annotation and comparative genomics using standard bioinformatics software tools (FastQC, FastP, SPAdes, Unicycler, Flye) 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 three-day-course will be separated into five sessions. Session I in the afternoon of day one, session II and III, and session IV and V in the morning and afternoon of day two and three, respectively.

Session I will provide a general introduction into the field of genome assembly, the reconstruction of the genomic DNA sequence from sequencing reads. This session gives an introduction to the main concepts, algorithms and tools, and peculiarities for de novo genome assemblies using short and long read sequencing reads. The course also focuses on the quality assessment of the sequencing data and introduces quality metrics to compare different assembly results.

In session II, the participants will gain practical experiences in a hands-on session. Assembly methods for short reads and long reads will be covered.

QA/QC of raw sequencing data
Assembly concepts and algorithms
QA/QC of assembled genomes
Hands-on Computing assemblies
In session III, the basic principles of regional and functional genome 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.

In session IV, there will be a short introduction into genome submission to INSDC sequence databases. We will demonstrate how to prepare, validate, and submit genome sequences to the ENA database by using the tool Webin-CLI. Afterwards, 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
In session V, the participants will gain practical experience in a hands-on session. All aspects of the EDGAR platform will be covered and features of EDGAR will be show-cased in detail.

Last but not least, there will be a wrap-up to discuss the presented tools and workflow and participants are encouraged to discuss open questions and practical issues.

Following all afternoon sessions, there will be time for custom data analysis consulting. Participants are encouraged to bring their own data which needs to be analyzed and/or discussed with the bioinformatics experts of the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi).

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

Agenda:

Wednesday (24.06.2026):

Afternoon session: Genome assembly (Oliver Rupp)
12:00 – 13:00 Arrival of participants
13:00 – 13:15 Welcome & introduction
13:15 – 14:30 Introduction to genome assembly Part 1 - Assembly basics
14:30 – 15:00 Coffee Break
15:00 – 16:30 Introduction to genome assembly Part 1 - Assembly strategies (short reads, long reads and hybrid)

Thursday (25.06.2026):

Morning session: Genome assembly hands on (Oliver Rupp)
09:00 – 10:30 Genome assembly hands on Part 1
10:30 – 11:00 Coffee Break
11:00 – 12:00 Genome assembly hands on Part 2
12:00 – 13:00 Lunch

Afternoon session: Genome annotation (Oliver Schwengers)
13:00 – 15:00 Introduction to genome annotation
15:00 – 15:30 Coffee Break
15:30 – 16:30 Bacta hands on

Friday (26.06.2026):

Morning session: Comparative Genomics (Jochen Blom)
09:00 – 09:45 NCBI/ENA genome submission
09:45 – 10:00 Coffee Break
10:00 – 12:00 Introduction to EDGAR platform
12:00 – 13:00 Lunch

Afternoon session: Comparative Genomics (Jochen Blom)
13:00 – 14:00 EDGAR Hands on
14:00 – 14:30 Wrap-up and goodbye

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