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bioRxiv · 10.64898/2026.03.28.714822

methbiome: reference-based DNA methylation profiling of long-read metagenomic data

Costeira, R.·Eustratiou Wong, E.·Bell, J. T.
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Abstract

SummaryLong-read DNA sequencing technologies collect base modification information, but their capacity to profile epigenetic signals has not been widely explored within metagenomic context. Here, we present a novel pipeline consolidating key steps of meta-epigenomic profiling. methbiome can process both Oxford Nanopore and PacBio long-reads within a reference-based framework, facilitating cross-platform and between-sample comparison of DNA methylation signals in whole microbiomes. The tool is applicable to both microbial communities and isolates, for analyses within both methylation motifs as well as out-of-motif contexts, and can be used in metaepigenome-wide association studies. Availability and Implementationmethbiome was implemented using Snakemake and is available on GitHub (github.com/ricardocosteira/methbiome).

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Costeira, R., Eustratiou Wong, E., Bell, J. T.. 2026-03-30. methbiome: reference-based DNA methylation profiling of long-read metagenomic data. https://doi.org/10.64898/2026.03.28.714822

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