Bioinformatics pipeline for the antimicrobial resistance (AMR) analysis of hospital wastewater metagenomic samples
Welcome to ATTACK-AMR - a bioinformatics pipeline for analysis of hospital wastewater antimicrobial resistance metagenomic data.
This pipeline requires the package manager Conda and the workflow management system Snakemake. Additional dependencies not handled by Snakemake are described in Section 1.3.
$ curl -sL \
"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" > \
"Miniconda3.sh"
$ bash Miniconda3.sh
$ conda update conda
$ rm Miniconda3.sh
$ conda install wget
$ conda config --add channels conda-forge
$ conda update -n base --all
$ conda install -n base mamba
$ mamba create -c conda-forge -c bioconda -n snakemake snakemake
This creates an isolated enviroment containing the latest Snakemake. To activate it:
$ conda activate snakemake
To test snakemake:
$ snakemake --help
Install git and gawk. We require gawk to process the filtering stage of our databases.
$ mamba install git
$ mamba install gawk
Download ATTACK-AMR from the online repository, or using the command line:
$ git clone https://github.com/bioinfodlsu/attack_amr
The pipeline requires, at the very least: (1) Metagenomic sequences (sample sequences can be downloaded at ENA, and (2) reference protein databases for (Resfinder, MGE). These and other input parameters are specified via a YAML-format config file -- config.yaml is provided in the config folder.
After constructing a config.yaml file and with the snakemake conda environment you created earlier activated, you can call the pipeline from the top-level directory of ATTACK-AMR:
$ cd attack_amr
$ snakemake --use-conda --cores all
Outputs are stored the top-level directory of ATTACK-AMR.