The 2023 Workshop on Genomics is being held 14-27th of May, 2023 in Český Krumlov, Czech Republic. This is the 12th time the Workshop of Genomics will be held in the Czech Republic, and the second time it will be organised in spring time. Applications are now closed, but we will likely be holding the 2024 Workshop on Genomics in January (7th – 20th January). Please Join Our Newsletter (bottom of this page) to get announcements on future workshops.

Our philosophy is to train participants in the most relevant topics in genomics, in a vibrant, immersive and inclusive environment. The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyse and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilising modern sequencing data. While the Workshop on Genomics topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. genome assembly, genome annotation, transcriptomics, metagenomics, population genomics).

Get ready for May 2023!

Many important details can be read on our FAQ page and our Housing and Transportation page 

Connecting to your instance tutorial, transferring files tutorial

Instance addresses (check every day for your new one!)

Workshop map

Check here to view Faculty / Organiser / Instructor arrival and departure dates. Check out our Faculty for 2023 here and our Instructors for 2023 here 

As is tradition, we will be having a T-shirt competition! Best T-shirt design will feature on the Workshop on Genomics 2023 T-shirts – get designing!

Workshop on Genomics 2023 BINGO!

Faculty lunches sign-up sheet

Our Code of Conduct contact points are Josie Paris & Joan Ferrer Obiol

Group photo!

Feedback email – [email protected]


Week 1 : 14-21 May, 2023

Date Day Time Presenter Topic LOCATION
14th May Sunday 18 – 22 Everyone Reception Hotel Zlaty Andel
15th May Monday 09 – 12

Josie Paris

Daniel Kintzl

Introduction and Orientation

Town Services

Town Theatre
  Monday 14 – 17 Mike Zody Sequencing Technology and Study Design Town Theatre
  Monday 19:30 – 22 Everyone Scientific Speed Networking Egon Schiele Museum
16th May Tuesday 09 – 12 Workshop Team Dreams, fantasy dreams and genomics Town Theatre
  Tuesday 14 – 17 Mercè Montoliu Nerín

AMI introduction


House of Prelate
  Tuesday 19 – 22 Mercè Montoliu Nerín UNIX House of Prelate
17th May Wednesday 09 – 12 Mike Zody Alignment (Lab) House of Prelate
  Wednesday 14 – 17 Erik Garrison Variant Calling (Lab) House of Prelate
  Wednesday 19 – 22 Fritz Sedlazeck Structural Variants (Lab) House of Prelate
18th May Thursday 09 – 12 Camille Marchet & Antoine Limasset Genome Assembly: theory and principles Town Theatre
  Thursday 14 – 17 Marcela Uliano-Silva Genome Assembly: from reads to a genome (Lab) House of Prelate
  Thursday 19 – 22 Marcela Uliano-Silva Genome Assembly: from reads to a genome (Lab)   House of Prelate
19th May Friday 09 – 12 Katharina Hoff & Natalia Nenasheva Genome Annotation (Lab) House of Prelate
  Friday 14 – 17 Katharina Hoff & Natalia Nenasheva Genome Annotation (Lab) House of Prelate
  Friday 19 – 22 Guy Leonard & Josie Paris Genomics Adventure House of Prelate
20th May Saturday 09 – 12 Erik Garrison Pangenomics (Lab) House of Prelate
  Saturday 14 – 15 Rayan Chikhi BIG Data House of Prelate
  Saturday 15 – 17 Everyone Open Lab / Round Table Discussions House of Prelate
  Saturday 18 – 22 Everyone

Town Tour


Town Square 

Depo (map)

21st May Sunday All Day Everyone Free Day Up to you!

Week 2 : 22-27 May, 2023

Date Day Time WHO Topic FORMAT
22nd May Monday 09 – 12 Rob Waterhouse

Comparative Genomics (Lab)

House of Prelate
  Monday 12 – 14 Everyone! (also Faculty Lunches) Workshop on Genomics picnic! 🌞 Monestary Gardens
  Monday 14 – 17 Francesco Cicconardi Comparative Genomics (Lab) House of Prelate
  Monday 19 – 22 Workshop Team

R & ggplot2


Solutions R Markdown

House of Prelate
23rd May Tuesday 09 – 12 Rosa Fernández Phylogenomics (Lab) House of Prelate
  Tuesday 14 – 17 Brian Haas Transcriptomics House of Prelate
  Tuesday 19 – 22 Rachel Steward Differential Gene Expression  (Lab) House of Prelate
24th May Wednesday 09 – 12 Sonya Dyhrman

Genomics in the Ocean (Part 2)

Town Theatre
  Wednesday 14 – 17 Aitor Blanco Miguez & Paolo Manghi

Metagenomics & Metatranscriptomics

MetaPhlAn Github

HUMAnN Github

House of Prelate
  Wednesday 19 – 22 David Barnett

Microbiome Analysis

Exercise 1

Exercise 2

House of Prelate
25th May Thursday 09 – 12 Evan Eichler Genome Structural Variation Egon Schiele Museum
  Thursday 14 – 17 James Whiting Population Genomics (Lab) House of Prelate
  Thursday 19 – 22 Doug Scofield Best Practices in Handling Genomic Data House of Prelate
26th May Friday 09 – 12 Chris Wheat

Lies, Damn Lies, and Genomics (Part 2)

Egon Schiele Museum
  Friday 14 – 17 Everyone Round Table Discussions, Tshirts and Certificates Egon Schiele Museum
  Friday 19:30 – 22 Everyone End of Workshop Party You Decide!
27th May Saturday All Day Everyone Departure  

Workshop Information

The Workshop registration fee is $1,950. We provide 90 hours of teaching during the two week workshop. Our price is therefore approximately $22 an hour. Note that this amount does not cover travel, lodging or boarding.

Many important details regarding fees and other information can be read on our FAQ page. 

The Workshop on Genomics 2023 is organised by:

Director Josephine Paris, Marche Polytechnic University, Italy

Co-Director (Course Engineer) Rayan Chikhi, Institut Pasteur, France

Co-Director (Faculty Liaison) Joan Ferrer Obiol, University of Milan, Italy

Lead Developer Guy Leonard, University of Oxford, UK

Head Teaching Assistant Mercè Montoliu Nerín – Uppsala University, Sweden

Český Krumlov Coordinator Daniel Kintzl

Coordinator Scott Handley, Washington University, US

Assisted by the Scientific Advisory Board:

Bill Cresko, University of Oregon, US

Sonya Dyhrman, Columbia University, US

Rosa Fernández, Institute of Evolutionary Biology CSIC-UPF, Spain

Sophie Shaw, All Wales Medical Genomics Service, UK

Alexander Suh, University of East Anglia, UK and Uppsala University, Sweden (Soon University of Bonn, Germany)  

Emiliano Trucchi, Marche Polytechnic University, Italy

Chris Wheat, Stockholm University, Sweden