ejurga/mob-rgi-nf

A nextflow pipeline to detect AMR determinants and mobile genetic elements.

MOB-RGI-NF

A NextFlow pipeline to identify antimicrobial genes and plasmids from genomic sequence data

Introduction

Plasmids are mobile genetic elements, and are often significant carriers of antimicrobial resistance genes. MOB-suite is a tool that is used to reconstruct and type plasmid sequences from whole genome sequence data. However, it does not identify AMR elements on identified plasmid sequences. The Resistance Gene Identifier (RGI) is a suite of tools that uses the Comprehensive Antimicrobial Database (CARD) to identify AMR determinants from whole genome sequence data. This pipeline serves as the union of these two tools, and therefore allows for the identification of AMR determinants present on mobile genetic elements from a given set of whole genome sequence data.

Overview

The nextflow script download_databases.nf is used to download the databases used by RGI and MOB-suite (if needed).

The nextflow script pipeline.nf runs both tools on a provided set of sequences. Both RGI and MOB-suite output their results in the form of tabular files. These results are merged, associating each detected AMR determinant with MOB-suite's results. This enables the user to identify if the AMR determinants are present on the chromosome, or on a plasmid. If multiple samples are passed to the program, the results will be collated into a single table.

Installation

Dependencies:

• NextFlow
• If using conda profile:
  • Conda
  • Mamba
• If using docker profile:
  • Docker

Usage

Clone this pipeline into a working directory.

Download databases

Both MOB-suite and RGI require databases to be downloaded in order to run the tools. MOB-RGI-NF provides a pipeline to download the databases if the user does not already have them. You may specify --download_mobDB to download the MOB-suite databases, --download_card_json to download the CARD json file, or --download_all to download both.

nextflow run download_databases.nf \
    -profile [conda|docker] \
    --download_all

By default, this command will download both databases into a databases folder in nextflow's work directory. This keeps the databases out of the way and prevents them from being deleted when nextflow runs are cleaned during analyses.

However, the user can specify their own locations instead. In this case, make sure to also specify the location of these databases when running the analysis pipeline.

nextflow run download_databases.nf \
    -profile [conda|docker] \
    --download_all \
    --mobDB "/path/to/mobDB/directory" \
    --card_json "/path/to/card/directory"

By default, MOB-RGI-NF will not overwrite the databases if it detects that they are already installed at the given path; set --overwrite to overwrite the existing databases if needed.

Detect AMR determinants and plasmids

Basic Usage

Use the script pipeline.nf to run mobSuite and RGI. The input should be assembled contigs. Use a bash glob to designate multiple sequences to be run by the pipeline. Note that the:wq file names will be used to designate sample ID.

Make sure to select a run profile, depending on the container you want to use. Currently conda (using mamba) and docker are supported. The pipeline will handle downloading and initializing the containers. Therefore, the very first run will take some time as the proper containers are downloaded.

nextflow run pipeline.nf \
    -profile [conda|docker] \
    --contigs "dir/to/sequences/*.fasta"

This command assumes that the databases have first been downloaded into the default directory by the download_databases.nf pipeline. Otherwise, specify the location of the databases. Use the option --mobDB to specify the path to the parent directory of the MOB-suite databases, and --cardDB to specify the path to the card.json file

The results will be collected in the directory results in the project directory by default. This can be changed with the option --outDir.

Detecting only AMR on plasmids

By default, MOB-RGI-NF will run RGI on all the contigs in a provided fasta file. This means it will detect AMR determinants present on the chromosome, as well as those on plasmids. Since RGI and MOB-suite can be run separately, the pipeline will use both tools in parallel, and merge the results at the end. If you are only interested in AMR determinants on plasmids, the option --plasmids_only can be supplied. This will run RGI only on contigs determined by MOB-suite to be from plasmids, and will significantly decrease the time it takes to run RGI. However, it means that RGI cannot be run parallel to MOB-suite, and so the actual time to completion of the pipeline may not actually be shorter, unless many samples are being processed at the same time.

Visuals

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mob-rgi-nf's Issues

Add support for singularity

Add support for singularity, for easy running on clusters.

Add a help message to download_databases.nf

Simply needs a help message.