Cansdale, Annabel and Chong, James P J orcid.org/0000-0001-9447-7421 (2024) MAGqual:a stand-alone pipeline to assess the quality of metagenome-assembled genomes. Microbiome. 226. ISSN 2049-2618
Abstract
BACKGROUND: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted. RESULTS: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards. CONCLUSIONS: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2024. |
Keywords: | Metagenomics/methods,Metagenome,Software,Microbiota/genetics,High-Throughput Nucleotide Sequencing/methods,Bacteria/genetics,Humans |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Biology (York) The University of York > Faculty of Social Sciences (York) > Social Policy and Social Work (York) > York Environmental Sustainability Institute |
Depositing User: | Pure (York) |
Date Deposited: | 11 Nov 2024 11:20 |
Last Modified: | 03 Jan 2025 00:19 |
Published Version: | https://doi.org/10.1186/s40168-024-01949-z |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1186/s40168-024-01949-z |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:219461 |