Mar 29, 2021

Online course: Genome assembly and annotation

ELIXIR in collaboration with NORBIS are pleased to announce an advanced online course about genome assembly and annotation. The course is aimed at researchers interested in learning more about genome assembly and annotation.

It will include an introduction to 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.

Time: May 3rd - May 7th 2021 - see registration below

Place: Online

Duration: 09.00 - 16.00

Prerequisites: Mandatory to complete a short command line course prior to the event. This will be made available to enrolled participants

Special notes: The course is limited to 25 people, and maximum 2 participants per national ELIXIR node (except Norway which allows participants from NORBIS). The course is an advanced course. Based on the information collected upon registration, the course organizers will enroll participants

Registration: The registration is open from March 30th to April 19. Please follow this link to register for the course. You will be able to access the course after you register and your registration is approved by the course organizers.

Confirmation to accepted participants: Will be sent out April 26.

Course certificate: Each participant will receive a certificate confirming their participation after the course

Course fee: The course is free of charge

Course organizers: Christophe Klopp (FR), Lucile Soler (SE), Mahesh Binzer-Panchal (SE), Nima Rafati (SE), Tomas Larsson (SE), Henrik Lantz (SE), Brane Leskosek (SL), Marko Vidak (SL) and Erik Hjerde (NO)

We wish to provide high quality in our training events, and are dependent on your feedback. We therefore encourage you to complete the survey that we provide with this course.

Feel free to contact us if you have any questions regarding the event.


Tentative schedule

Day 1
Welcome and introduction
Practical: One hour to get all on board
Lecture: Introduction to genome assembly and annotation
Lecture: Read QC - Quality Assessment of sequencing data
Practical: Read QC

Day 2
Lecture: Gathering knowledge before the assembly, assemblies and assembly polishing
Practical: Long read assembly and polishing
Lecture: Assembly Validation
Practical: Assembly Validation

Day 3
Lecture/Practical: Hi-C sequencing
Project discussion and catch-up with previous exercises
Walkthrough of earlier exercises and wrap-up

Day 4
Lecture: Method in Structural Annotation
Lecture : Structural annotation
Practical : Structural annotation
Abinitio annotation
Gathering data
Evidence based annotation with maker
Abinitio training
Abinitio evidence-driven annotation with maker

Day 5
Practical : Structural annotation
Practical : Annotation assessment
Practical: Manual curation
Lecture: Functional Annotation
Practical: Functional Annotation
Practical : Submission to DB
Lecture: Bacterial Annotation
Practical: Bacterial Annotation

Discussion and Summary