BiG-MEx

BiG-MEx: a tool for the mining of Biosynthetic Gene Cluster (BGC) domains and classes in metagenomic data. It consists of the following modules:

1. bgc_profiler: BGC protein domain annotation and BGC class abundance predictions
2. bgc_dom_div: BGC domain-based diversity analysis.

Citation

Pereira-Flores, E., Buttigieg, P. L., Medema, M. H., Meinicke, P., Glöckner, F. O. and Fernandez-Guerra, A.. (2021). Mining metagenomes for natural product biosynthetic gene clusters: unlocking new potential with ultrafast techniques. bioRxiv doi: 10.1101/2021.01.20.427441

Installation

BiG-MEx consists of three docker images:

1. bgc_profiler
2. meta_bgc_dom_div
3. merge_bgc_dom_div

Before running BiG-MEx it is necessary to install either docker or singularity. Then, simply download the corresponding scripts from below:

Using docker:

run_bgc_profiler.bash
run_bgc_dom_div.bash

Using singularity:

run_bgc_profiler.bash
run_bgc_dom_div.bash

All container images will be downloaded automatically the first time you run the scripts.

Documentation

These run_bgc_*.bash scripts run the container images, which include all the code, dependencies, and data used in the analyses. When using docker, if your user is not in the docker group in Linux or Mac OS, the run_bgc_*.bash scripts have to be executed with sudo.

1. bgc_profiler

This module first runs UProC using a BGC domain database. It takes as an input metagenomic unassembled data and outputs the BGC domain counts profile. Then, based on the bgcpred R package and using the BGC domain counts as predictor variables, it computes the BGC class abundance profile.

See help

./run_bgc_profiler.bash --help

2. bgc_dom_div

The bgc_dom_div has two different modes: metagenome (meta) and merge. The first mode has the objective of analyzing the BGC domain diversity in metagenomic samples. This analysis consists of estimating the operational domain unit (ODU) diversity, blasting the domain sequences against a reference database, and placing the domain sequences onto reference phylogenies. The merge mode integrates the metagenome diversity results of different samples to provide a comparative analysis.

See help

./run_bgc_dom_div.bash meta --help

./run_bgc_dom_div.bash merge --help

See the wiki for further documentation.