Investigating the landscape of antibiotic resistance genes and their mobile genetic elements carriers across diverse taxa and environments using long-read metagenomics sequence data

This serves as a guide to run the analysis pipeline written in Snakemake.

Installation for Snakemake

This Snakemake 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 the online repository, or using the command line:

$ git clone https://github.com/bioinfodlsu/long-read-metagenomics-arg-mge

2. Quickstart Usage Guide

2.1. Running the pipeline

With the snakemake conda environment activated, you can call the pipeline from the top-level directory:

$ cd long-read-metagenomics-arg-mge
$ snakemake --use-conda --cores all

In case of errors encountered relating to the use of conda environments, please use the following command:

$ snakemake --use-conda --cores all --conda-frontend conda