Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.

ABSTRACT: Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriop

SUBMITTER: Langenfeld K 

PROVIDER: S-EPMC11878531 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature