cgemetagenomics

This tool was developed for analysing stool/microbiome sample where microbes and AMR might be found.

Installation

The following Conda channels are required:

conda config --add channels defaults

conda config --add channels bioconda

conda config --add channels conda-forge

Mamba can be installed with:

conda install -c conda-forge mamba

For a fast install of cgemetagenomics, use mamba: mamba install -c genomicepidemiology cgemetagenomics

Datebase

Download the cge_db database:

wget https://cge.food.dtu.dk/services/great-life/cge_db.tar.gz

tar -xvzf cge_db.tar.gz

sudo mkdir -m 777 /var/lib/cge

sudo mkdir -m 777 /var/lib/cge/database

mv cge_db /var/lib/cge/database/cge_db

Usage

Standard Usage: cgemetagenomics -i <input_file> -o <output_file>

If your cge_db is not stored in /opt/cge/cge_db: cgemetagenomics -i <input_file> -o <output_file> -db_dir <path_to_cge_db>

Help Message: cgemetagenomics -h