Evaluating limitations of quantitative metagenomics with synthetic dsDNA and ssDNA standards

Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. We used synthetic ssDNA and dsDNA standards to develop a quantitative metagenomic approach, called QuantMeta, that accounts for detection and quantification limitations. QuantMeta applies entropy-based detection limits that incorporate both read distribution and coverage and sets read depth variability thresholds to detect and correct quantification errors caused by non-specific mapping and assembly errors. In proof-of-concept wastewater metagenomes, we compared QuantMeta-based total virus concentrations, as well as polyomaviruses and crAss-like phages of interest, to those of traditional, low-throughput methods. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target concentrations. ### Competing Interest Statement The authors have declared no competing interest. * ssDNA : single-stranded DNA dsDNA : double-stranded DNA viromes : viral metagenomes ddPCR : droplet digital PCR qPCR : quantitative PCR