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

  • Search mechanisms available against catalogues

  • How MAG catalogues fit into the rest of the MGnify service

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 services:API practical.

The practical will use a Jupyter Notebook.

Fetch the code repository

cd /home/training
git clone https://github.com/EBI-Metagenomics/genome-resolved-metagenomics-2022.git

Do you have MAGs?

info 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, there should already be some in /home/training/Binning/contigs.fasta.metabat-bins2000.bak.

If you accidentally damaged those files, you can copy some from the shared drive:

cp -r /media/penelopeprime/Metagenomics-Nov21/Day4/day-4-example-mag-bins/* /home/training/Binning/contigs.fasta.metabat-bins2000.bak/`

Opening the Jupyter notebook

action Open a new Terminal. There should be a Terminal application icon in the lefthand menubar.

action Type these commands to enter the repository:

cd /home/training/genome-resolved-metagenomics-2022

conda activate metagenomics

info That should have worked, but if you got an error you’ll need to create the environment:

conda create --n metagenomics python=3.9

conda activate metagenomics

pip install -r requirements.txt

action To open the notebooks, run:

jupyter-lab course.jupyterlab-workspace

action And follow the instructions to access the notebook using the Chromium browser

Today’s Notebook is “Day 4”.