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.
| Information | Description |
|---|---|
| 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. |
| Confirmation to accepted participants: | Will be sent out April 26. |
| Course certificate: | Each participant will receive a certificate |
| 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