attack_amr

Bioinformatics pipeline for the antimicrobial resistance (AMR) analysis of hospital wastewater metagenomic samples

0. Introduction

Welcome to ATTACK-AMR - a bioinformatics pipeline for analysis of hospital wastewater antimicrobial resistance metagenomic data.

1. Installation

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.

1.1. Install Miniconda

$ 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

1.2. Install Mamba

$ conda config --add channels conda-forge
$ conda update -n base --all
$ conda install -n base mamba

1.3. Install Snakemake

$ 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

1.4. Install Additional Dependencies

Install git and gawk. We require gawk to process the filtering stage of our databases.

$ mamba install git
$ mamba install gawk

1.5. Download the pipeline

Download ATTACK-AMR from the online repository, or using the command line:

$ git clone https://github.com/bioinfodlsu/attack_amr

2. Quickstart Usage Guide

2.1. Input

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.

2.2. Running the pipeline

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

2.3. Ouput

Outputs are stored the top-level directory of ATTACK-AMR.