In a rather belated piece of dissemination, our congratulations to the authors of a paper published last year which concerns one of our recurring topics.
From its inception EBNet has championed the importance of complex microbial communities for environmental protection and remediation, whether in engineered systems or the open environment. Not only do many of our current highly effective biotechnologies depend on these communities: they also contain undiscovered potential in species and dynamic metabolic interactions (see the Microbes in Wastewater Treatment animation for an enjoyable high-speed take on this topic).
Understanding these communities is challenging because of their extreme complexity, while some of the species in them are not readily characterised as they cannot be cultured in the lab, or we lack the necessary tools for manipulation. This has led to the growing popularity of metagenomics approaches, in which the genome of whole microbial communities is sequenced. This too can be challenging due to the vast data sets involved, and the variable quality of metagenome-assembled genomes (MAGs). To address this, the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard has been proposed as a framework for classifying MAG quality and reporting specified metadata on each MAG.
The MAGqual (Metagenome-Assembled Genome qualifier) pipeline was developed as a tool to facilitate this evaluation on a large scale. MAGqual enables the user to pass in MAGs generated by metagenomic binning software and quickly assess the quality of these bins according to the MIMAG standards. The paper presents the pipeline and demonstrates its effectiveness at determining metagenomic dataset quality and presenting MIMAG and other statistical parameters.
Prof James Chong, co-Lead of EBNet’s Bioinformatics WG, said: “The MIMAG standards support reproducibility in metagenomic studies, but are not yet widely applied. Hopefully MAGqual will help to improve this, by providing an easy way to benchmark new metagenomic binning software or analysis methods. The MAGqual pipeline supports FAIR (findability, accessibility, interoperability and reusability) principles by generating comparable metrics for datasets from different sources”.
An earlier version of this work was presented by Annabel Cansdale at EBNet’s 2024 conference, and a video abstract is also available here.
MAGqual is open-source to promote accessibility, community development and ease of updating. It is built in Snakemake, R and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual.
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes. Cansdale, A. and Chong, J.P., 2024. Microbiome, 12(1), p.226.