MAGScoT – a fast, lightweight, and accurate bin-refinement tool.

Abstract

Motivation

Recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic data is an important task for the comprehensive analysis of microbial communities from variable sources. Single binning tools differ in their ability to leverage specific aspects in MAG reconstruction, the use of ensemble binning refinement tools is often time consuming and computational demand increases with community complexity. We introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality MAGs from the output of multiple genome-binning tools.

Results

MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption.

Availability

MAGScoT is available via GitHub (https://github.com/ikmb/MAGScoT) and as an easy-to-use Docker container (https://hub.docker.com/repository/docker/ikmb/magscot).

Supplementary information

Supplementary data are available at Bioinformatics online. All scripts to produce the binning results and the subsequent refinement are available via GitHub (https://github.com/mruehlemann/MAGScoT_benchmarking_scripts).