MetaResist

Pipeline for resistome analysis and AMR prediction from metagenomic sequencing data.

Usage

Step 1: Install Snakemake

Snakemake is best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it can be installed via Mambaforge. For other options see here.

Given that Mamba is installed, run

    mamba create -c conda-forge -c bioconda --name snakemake snakemake

to install Snakemake in an isolated environment. For all following commands ensure that this environment is activated via

    conda activate snakemake

Step 2: Clone workflow

First, create an appropriate project working directory on your system and enter it:

    WORKDIR=path/to/project_workdir
    mkdir -p ${WORKDIR}
    cd ${WORKDIR}

In all following steps, we will assume that you are inside of that directory.

Second, to clone the full workflow run:

    git clone https://github.com/IKIM-Essen/MetaResist

Step 3: Install required tools

Install sra-tools for downloading SRA samples:

    mamba install -c bioconda -c conda-forge sra-tools

Install peppy for handling PEP-based sample metadata:

    mamba install -c conda-forge -c bioconda peppy

Step 4: Download example SRA samples

Example SRA runs used for initial testing:

• SRR26321896 (Klebsiella pneumoniae)

Download the sample using prefetch and convert it to FASTQ format with fasterq-dump :

    prefetch SRR26321896
    fasterq-dump SRR26321896 --split-files --threads 8

For single-end data:

    gzip SRR26321896.fastq

Step 5: Prepare sample metadata

Edit the config/pep/samples.csv file to add your sample:

    sample_name,fastq
    SRR26321896,data/raw/SRR26321896.fastq.gz

Step 6: Run the workflow

Perform a dry-run first:

    snakemake -n

Run the workflow:

    snakemake --cores all --use-conda