Mamba installation and environment

Mamba is a reimplementation of Conda. It is a fast and reliable tool for installing bioinformatics software, including R packages.

Useful links:

Mamba GitHub: https://github.com/mamba-org/mamba
Miniforge (recommended installer): https://github.com/conda-forge/miniforge
Mamba documentation: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html

The recommended way to use Mamba is via Miniforge, which provides both conda and mamba commands.

Restarting the Practical

If you are restarting during or after the practical, use the commands in this box.

wget -r -np -nH --cut-dirs=3 -A "shotgun_meta.yml" https://cgr.liv.ac.uk/454/acdarby/LIFE750/
#wget -r -np -nH --cut-dirs=3 -A "shotgun_meta_clean.yml" https://cgr.liv.ac.uk/454/acdarby/LIFE750/

mamba env create -f shotgun_meta.yml
conda activate shotgun_meta

sudo apt install firefox
ktUpdateTaxonomy.sh

mkdir -p ~/kraken2_db
cd ~/kraken2_db
wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08_GB_20251015.tar.gz
tar -xvzf k2_standard_08_GB_20251015.tar.gz

1 Databases

Kraken2 database for this practical

For this practical, we will use a preformatted Kraken2 database suitable for laptop-based teaching.

We use the Standard-8 database (also known as MiniKraken2 v2), which contains a reduced set of reference genomes but provides reliable bacterial classification for this workshop.

Database index: https://benlangmead.github.io/aws-indexes/k2

The k2_standard_08_GB database is installed by the commands above.