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Source code for analysis of hospital wastewater metagenomic data

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attack_amr

Source code for analysis of hospital wastewater metagenomic data

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. All other dependencies are handled automatically by Snakemake.

1.1. Install Conda

Download Miniconda3 installer for Linux from here. Installation instructions are here. Once installation is complete, you can test your Miniconda installation by running:

$ conda list

1.2. Install Snakemake

Snakemake recommends installation via Conda:

$ conda install -c conda-forge mamba
$ mamba create -c conda-forge -c bioconda -n snakemake snakemake

This creates an isolated enviroment containing the latest Snakemake. To activate it:

$ mamba init
$ mamba activate snakemake

To test snakemake installation

$ snakemake --help

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Source code for analysis of hospital wastewater metagenomic data

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