MGnify Genomes Catalogues¶
In the presentation we will cover:
Recap of MAG generation
Overview of MGnify MAG Catalogues
Annotations available for catalogues and genomes
Metadata available for catalogues and genomes
Download files available for catalogues and genomes, via web, FTP, and the API
Search mechanisms available against catalogues
MAG Catalogues hands-on exercises¶
These exercises will again use the API (“Application programming interface”), showing how your scripts (e.g. Python or R) can talk to the MGnify database.
This builds on the exercises you looked at in the API practical.
The practical will use a Jupyter Notebook.
Do you have MAGs?¶
For the last few exercises, you need some MAGs. If you didn’t get as far as making your own MAGs in the MAG generation exercises, you can copy some we made earlier with this command in a Terminal:
cp -r /media/penelopeprime/Metagenomics-Nov21/Day4/day-4-example-mag-bins/* ~/mags
If you DID make your own, copy them to ~/mags
.
Opening the Jupyter notebook¶
Open a new Terminal. There should be a Terminal application icon in the lefthand menubar.
Type these commands to enter the repository:
cd ~/mgnify-ebi-2021
conda activate mgnify-ebi-2021
That should have worked, but if you got an error you’ll need to create the environment:
conda create --n mgnify-ebi-2021 python=3.9
conda activate mgnify-ebi-2021
pip install -r requirements.txt
jupyter-lab course.jupyterlab-workspace
Today’s Notebook is “Day 4”.