This repository contains course materials for a workshop on structural genome annotation with BRAKER and TSEBRA
Authors: Katharina Hoff
Contact: [email protected]
This course material is designed to work on resources of University of Greifswald.
In intranet (establish VPN connection if necessary, see https://rz.uni-greifswald.de/dienste/technische-infrastruktur/vpn/).
Go to https://apphub.wolke.uni-greifswald.de/ in Chrome/Chromium browser. Login with university credentials. Select "Bioinformatics". Note that there is a tiny arrow pointing downwards on the far right of "START". Click on that arrow to expand Advanced options. Select "CPU 6" and "RAM 10GB" before pressing the "START" button. On the bottom of the page, click on "Open" once the instance has booted (will take a little while). Your instance will open in a new browser tab.
If you don't have access to our AppHub but you do have a machine with Docker and root permissions, you can run the course container on your own machine as follows:
sudo docker run --rm -it -u 1000:0 -p 8888:8888 katharinahoff/bioinformatics-notebook:devel
Click on the link and continue to work in your web browsern (best use Chrome/Chromium).
Open a terminal window (black symbol with white dollar-underscore sign) and enter (press enter key after typing):
git clone https://github.com/KatharinaHoff/BRAKER-TSEBRA-Workshop.git
On the left, a folder BRAKER-TSEBRA-Workshop will appear in your "file navigator". That folder contains the JupyterNotebook for this course (GenomeAnnotation.ipynb).
- repeat library generation and repeat masking with RepeatModeler2/RepeatMasker (only theory)
- short read RNA-Seq to genome alignment with Hisat2 (only theory)
- application of BRAKER3 (structural genome annotation with short read RNA-Seq alignments & protein database)
- application of BRAKER1 (structural genome annotation with short read RNA-Seq alignments)
- application of BRAKER2 (structural genome annotation with protein database for small & medium sized genomes)
- application of GALBA (structural genome annotation with proteins of closely related species in large genomes)
- BUSCO assessment of predicted gene set
- running TSEBRA after BRAKER/GALBA
- preparing an assembly hub for the UCSC Genome Browser with MakeHub
The idea of a schedule is as follows:
- 9:00 - Start joining zoom
- 9:10 - Welcome & introductions (Padlet Link in Chat)
- 9:30 - Lecture on genome annotation with BRAKER & GALBA
- 10:30 - Coffee break
- 10:45 - Begin hands-on session for beginners
- 12:00 - Lunch break
- 13:00 - Continue hands-on session for beginners
- 14:00 - Coffee break
- 14:15 - For advanced learners: annotate Babesia duncani chromosome
- 15:15 - Wrap up of advanced learners' session
- 15:30 - End
Stefan Kemnitz from The University Compute Center at University of Greifswald (https://rz.uni-greifswald.de/dienste/allgemein/sonstiges/high-performance-computing/) kindly assisted in building the docker container. Lars Gabriel prepared materials for TSEBRA in 2022.