First release: June 13, 2024
Parkinson Lab's in-house MG pipeline. Setup: Need to download a few databases: https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm https://data.ace.uq.edu.au/public/CheckM_databases/
https://ecogenomics.github.io/GTDBTk/installing/index.html#installing-gtdbtk-reference-data WARNING: it's 84GB, and you need to unzip it yourself.
Also: use the sample config, and assign the 2 databases entries to the paths. special note for gtdbtk, use release220, and have the config point to it.
Also: your host fastas need to be indexed by BWA before use. else quackers will complain.