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Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.

Diego Alvarez Saravia·Adam Rosenbaum·Daniel Straub·Jim Downie·Maxime Borry·Greg Fedewa·Alexander Hübner·Daniel Lundin·Jeferyd Yepes-García·James McDonald·Sven Nahnsen·Linda Köhn·Roberto Uribe-Paredes·Marcelo A Navarrete·Christina Warinner·nf-core community·James A Fellows Yates
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Abstract

SUMMARY: nf-core/mag is a reproducible Nextflow pipeline for best-practice metagenomic de novo assembly and binning within the nf-core framework. Here we present a major update that adds support for long-read-only assembly and bin refinement, includes five new binning tools, expands taxonomic classification to viruses and eukaryotes, and improves bin quality evaluation with new tools and latest databases. Through sustained community-driven development spanning seven years and four primary curator teams, nf-core/mag remains actively developed as an open source workflow for metagenomic analysis, benefiting from contributions from across the broader metagenomics, nf-core, and Nextflow ecosystem. AVAILABILITY AND IMPLEMENTATION: The source code of nf-core/mag v5 is available on GitHub (https://github.com/nf-core/mag) under the open source MIT license, with v5.5.0 source code archived on Zenodo (https://zenodo.org/records/21735731). Documentation is viewable on the nf-core website (https://nf-co.re/mag).

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MetagenomicsSoftwareHigh-Throughput Nucleotide SequencingJournal ArticleResearch Support, Non-U.S. Gov't

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Diego Alvarez Saravia, Adam Rosenbaum, Daniel Straub, Jim Downie, Maxime Borry, Greg Fedewa, Alexander Hübner, Daniel Lundin, Jeferyd Yepes-García, James McDonald, Sven Nahnsen, Linda Köhn, Roberto Uribe-Paredes, Marcelo A Navarrete, Christina Warinner, nf-core community, James A Fellows Yates. 2026-08-31. Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.. https://doi.org/10.1093/bioinformatics%2Fbtag628

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