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Research article - Peer-reviewed, 2022

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

Krakau, Sabrina; Straub, Daniel; Gourle, Hadrien; Gabernet, Gisela; Nahnsen, Sven

Abstract

The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install-all dependencies are provided within containers-portable and reproducible. It is written in Nextflow and developed as part of the of-core initiative for best-practice pipeline development. All codes are hosted on GitHub under the of-core organization https://github.com/nf-core/mag and released under the MIT license.

Published in

NAR genomics and bioinformatics
2022, Volume: 4, number: 1
Publisher: OXFORD UNIV PRESS

    UKÄ Subject classification

    Genetics and Breeding

    Publication identifier

    DOI: https://doi.org/10.1093/nargab/lqac007

    Permanent link to this page (URI)

    https://res.slu.se/id/publ/123323