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de.NBI Microbial Genomics training course 20.-22.05.2019

Agenda for the 5th de.NBI Genomics training course 20.-22.05.2019


The first day will introduce software tools for the quality control of short read data. For conducting basic sequence read processing steps we will use our local Galaxy server. In the last session we will explain the basic approaches for genome assembly and run various genome assemblers:

  • Introduction to quality control
  • Automatic trimming of sequencing reads
  • The basics of genome assembly

On the second day we will take a closer look at the genome assembly results. Afterwards, we provide a comprehensive introduction to microbial genome annotation. Available tools and algorithms for the different genome analysis and annotation steps will be explained and used within Galaxy. The GenDB genome annotation pipeline will be presented as well as a new stand-alone high-throughput genome analyses pipeline (ASA3P) that can be used to process thousands of genomes on a single day:

  • The basic principles of region and function annotation
  • Genome annotation tools and pipelines in Galaxy
  • Manual and distributed genome annotation using GenDB
  • Introduction to the ASA3P software

The third day will give an introduction into comparative genomics with a focus on differential gene content analysis using the EDGAR platform.  The use of the BLAST score ratio values (SRVs) to measure the similarity between coding sequences and to assess orthology will be introduced. All features of EDGAR will be introduced in detail:

  • Genomic subset calculations (core-genome, pan-genome, singleton genes)
  • Core-genome-based phylogenetic analyses
  • Sequence based phylogeny
  • ANI, AAI
  • Statistical analyses (core/pan/singleton development plots)
  • The public EDGAR database

On all three days the program includes extensive hands-on training to allow participants to get familiar with the presented software. Participants can bring their own datasets that fit the topics of the workshop. The data can be analyzed in the hands-on sessions.

We have to demand a 30 Euro fee to cover our expenses for catering, apart from that the workshop is free.



To register for this training course please complete our registration form and send it with a short email to our contact address below so that we have all necessary details. Due to the fact that that the number of participants is limited to 20, we will schedule according on a first come first served basis.



Day 1: Quality control & genome assembly

  • 13:00 13:15   Welcome & introduction (Alexander Goesmann)
  • 13:15 – 13:30   Transfer of data sets
  • 13:30 – 15:00   Read quality control & trimming incl. hands-on session (Sven Griep, Oliver Rupp)
  • 15:00 – 15:30   Coffee Break
  • 15:30 – 17:00   Introduction to genome assembly incl. hands-on session (Sven Griep, Oliver Rupp)

Day 2: Microbial Genome Annotation

  •   9:00 – 10:30   Introduction to microbial genome annotation (Alexander Goesmann)
  • 10:30 – 11:00   Coffee Break
  • 11:00 – 12:30   Genome annotation with Galaxy & GenDB hands-on session (Sven Griep, Oliver Rupp, Tobias Zimmermann)
  • 12:30 – 13:30   Lunch
  • 13:30 – 14:30   Introduction to ASA3P (Oliver Schwengers)
  • 14:30 – 15:00   Coffee Break
  • 15:00 – 17:00   ASA3P practical session (Oliver Schwengers, Andreas Hoek)
  • 17:30                Optional: Tour to Gleiberg castle

Day 3: Comparative Genomics

  •   9:00 – 10:30   EDGAR (Jochen Blom)
  • 10:30 – 11:00   Coffee Break
  • 11:00 – 12:00   EDGAR hands-on (Jochen Blom, Sebastian Jaenicke)
  • 12:00 – 12:30   Course evaluation & closing remarks (all hands)

During the afternoon of the last day participants are invited to discuss open questions or individual projects or data sets with the course experts.


The de.NBI project is funded by the BMBF.
FKZ 031A532 — 031A540