Sammanfattning

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.

Publicerad i

NAR genomics and bioinformatics
2022, Volym: 4, nummer: 1
Utgivare: OXFORD UNIV PRESS

SLU författare

• Gourlé, Hadrien

  • Institutionen för husdjurens biovetenskaper, Sveriges lantbruksuniversitet
    

UKÄ forskningsämne

Genetik och förädling


Publikationens identifierare

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

Permanent länk till denna sida (URI)

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