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Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities

Heidelbach, S.; Dall, S. M.; Boejer, J. S.; Nissen, J.; van der Maas, L. N. L.; Sereika, M.; Kirkegaard, R.; Kousgaard, S. J.; Thorlacius-Ussing, O.; Jensen, S. I.; Hose, K.; Nielsen, T. D.; Albertsen, M.

2025-01-04 bioinformatics
10.1101/2024.04.29.591623 bioRxiv
Show abstract

DNA methylation is found across all domains of life but is a rarely used feature in recovery of metagenome-assembled genomes (MAGs). Recently, Oxford Nanopore introduced all context methylation detection models. We leveraged this to develop Nanomotif, which identifies and exploits methylation motifs for enhanced MAG recovery. We demonstrate how Nanomotif enables database-independent contamination removal from high-quality MAGs and host association of plasmids directly from Nanopore sequencing data in complex metagenomes.

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