Course in genome assembly and annotation

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A course is being organized in Prague, hosted by the Czech ELIXIR Node lead institute in cooperation with the nodes involved in ELIXIR-EXCELERATE task 10.3 “Capacity Building in Genome Assembly and Annotation”. Some of the most experienced assembly and annotation experts in Europe will be teaching at the course.

The course is aimed at researchers interested in learning more about genome assembly and annotation. It will include information useful for both the beginner and the more advanced user. We will start by introducing general concepts and then continue to step-by-step describe all major components of a genome assembly and annotation workflow, from raw data all the way to a final assembled and annotated genome. There will be a mix of lectures and hands-on practical exercises using command line Linux. After the course the participants will be aware of common practices and commonly used tools and be able to run assembly and annotation projects on their own.

Workshop Programme

Preliminary programme, note that details might change. We will confirm the final programme prior to the course start. Lunch and coffee breaks to be included at a later stage as well.

Day 1 Wednesday Oct 12

09.00     Welcome and presentation of experts and round of introduction by participants (Jiri Vondrašek, Henrik Lantz).
09.30     Lecture: Introduction to genome assembly and annotation (Henrik Lantz)
10.00     Coffee break
10.15     Lecture: Read QC (Mahesh Panchal)
11.00     Practical: Assembly QC
12.00     Lunch
13.00     Practical: Assembly QC cont
13.45     Lecture: Illumina assembly (Erik Hjerde)
14.45     Coffee break
15.00     Practical: Genome assembly using Illumina data
17.00     End

Day 2 Thursday Oct 13

09.00     Lecture – Long read technologies (Christophe Klopp)
10.00     Coffee break
10.15     Practical: PacBio assembly
12.00     Lunch
13.00     Project discussion
14.00     Lecture: Assembly validation (Martin Norling)
14.45     Coffee break
15.00     Practical: Assembly validation
19.00     Working Dinner at Restaurace pod Juliskou

Day 3 Friday Oct 14

09.00     Lecture: Structural annotation (Lieven Sterck)
10.00     Coffee break
10.15     Lecture: Annotation of transposable elements (Joelle Amselem)
11.15     Practical: Structural annotation
12.00     Lunch
13.00     Lecture: Functional annotation (Jacques Dainat)
14.00     Practical: Functional annotation and wrap-up
15.00     Coffee break
15.15     Practical: Functional annotation and wrap-up cont.
17.00     End

Working Dinner at Restaurace pod Juliskou

 After this course, what kind of support would you need to efficiently continue to work with your own data?

  • Looking at your own bioinformatics needs, what do you see as the greatest challenge in bioinformatics just now? Availability of compute resources? Training? Other?
  • What other types of courses would you like ELIXIR to offer?
  • Would you be interested in a short internship (1-2 weeks) at an expert bioinformatics center in another European country?


Institute of Organic Chemistry and Biochemistry AS CR
Flemingovo náměstí 2, Prague 6
Building A, 4th floor

See Google Map

The Institute carries out fundamental research in organic chemistry, biochemistry and related disciplines, focusing in particular on medical and environmental applications. The IOCB is also the Node representative and coordinator of the ELIXIR CZ infrastructure.


Jiří Vondrášek
Head of ELIXIR Czech Node
Phone: +420 220 183 267
Mobil: +420 739 309 016
Henrik Lantz
Course responsible – ELIXIR Sweden
Office: +46 (0)18-4714230
Hana Pergl Sustkova
Project Manager ELIXIR CZ
Office: +420 220 183 201
Mobile: +420 773 791 515
Tereza Votrubova
Assistant ELIXIR CZ
Office: +420 220 183 126

Entry requirements

Some experience in Linux command line is needed to participate in the practical exercises. Experience of Next Generation Sequencing data is recommended. Scripting/programming experience not necessary.

It is expected that you bring your own laptop for the workshop.


Registration is closed. 
Registration is limited to max 30 participants due to the training room capacity.


Travel expenses and lodging need to be covered by each participant individually. Czech Node will cover the meeting costs.


Bed and breakfast type of accommodation has been pre-booked with the below mentioned hotels in the vicinity of the workshop venue. Variety of rooms is available, approximate cost for single room is 50-60€, for double room 70-80€.

If you want to have the accommodation organised by us, please fill in the following Doodle poll by 20.9.2016 indicating the dates of your stay and room preference. Room preference will be taken into consideration, but is subject to availability.

If you want to share room with other participant, please inform us by email to

Lodging details (exact location and dates) will be confirmed to each participant by end September.

Unfortunately the organizing team is unable to handle accommodation requests after Sep 20th. Do not hesitate to contact us though, if you struggle with hotel booking after this date.

Vila Lanna
V sadech 1
160 00 Prague 6
Czech Republic
See Google Map

Penzion Marna
Na Marně 9
160 00 Prague 6
Czech Republic

See Google Map

Gotthardská 54/2
160 00 Prague 6
Czech Republic

See Google Map

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