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

SLU Authors

• Gourlé, Hadrien

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

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