wpmr/drax repository overview

⁠D⁠etecting R⁠esistome A⁠ssociated taX⁠a

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DRAX is currently under active development -- please check back soon.

⁠Overview

DRAX is a Nextflow⁠ pipeline to detect resistome associated taxa in metagenomes. It identifies Antimicrobial Resistance Genes (ARGs) using GROOT⁠, extracts the genomic environment of each ARG using Metacherchant⁠ and then performs taxonomic classification of assembled environments. Further pipeline steps and full documentation are being added.

⁠Installation

⁠Bioconda

For ease of use, the DRAX pipeline is called by a wrapper script that allows you to either download the required reference data, run the DRAX Nextflow⁠ pipeline or update the pipeline. It is easiest to install DRAX using Bioconda⁠:

conda install drax -c bioconda

⁠Containers

You can also run DRAX using containers instead of conda. This will bypass the wrapper script so you will need to download the required reference data yourself.

# Install Nextflow
curl -s https://get.nextflow.io | bash

# Run DRAX with Docker
./nextflow run will-rowe/drax --reads 'tests/*R{1,2}.fq.gz' -profile docker

# OR run DRAX with Singularity
./nextflow run will-rowe/drax --reads 'tests/*R{1,2}.fq.gz' -with-singularity 'docker://wpmr/drax'

⁠Quick Start

The first time you use DRAX, you will need to get the required data:

drax get

• this will download several databases (masked hg19 for decontamination, ResFinder for GROOT, Kaiju RefSeq DB...)
• it can take a little while (databases total ~10GB compressed)
• you only need to do this once
• the default directory is ./DRAX-files but you can rename/move it later
• this command will also update the pipeline to the most current version

Now you can run DRAX:

drax --reads 'tests/*R{1,2}.fq.gz' --refData ./DRAX-files

For a full list of options, just run:

drax --help

Also, read the documentation⁠ for a more detailed overview of DRAX.

⁠Workflow

⁠Documentation

The DRAX pipeline comes with documentation about the pipeline, found in the docs⁠ directory. This is still being added to as the pipeline is developed.