This repository contains course materials for a workshop on structural genome annotation with BRAKER and TSEBRA

Authors: Katharina Hoff & Lars Gabriel

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 "RESPONSE". 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/response-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
• short read RNA-Seq to genome alignment with Hisat2
• application of BRAKER1 (structural genome annotation with short read RNA-Seq alignments)
• application of BRAKER2 (structural genome annotation with protein database)
• merging BRAKER1 and BRAKER2 gene sets with TSEBRA
• BUSCO assessment of predicted gene set
• preparing an assembly hub for the UCSC Genome Browser with MakeHub

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.