De novo likelihood-based measures for comparing metagenomic assemblies

Metagenomic assemblers inherit all the difficulties of traditional single genome assembly, but with the additional complexity of trying to resolve assemblies of closely related species with drastically varying abundances. Assessing and comparing the quality of single genome assembly still relies on the availability of independently determined standards, such as manually curated genomic sequences. These standards are often not possible in metagenomic projects, where a large portion of the organisms and strains are novel. Thus, we must rely on de novo methods for assessing and comparing assembly qualities. Here we describe an extension to our de novo LAP framework that takes into account abundances of assembled sequences to accurately and efficiently evaluate metagenomic assemblies. We have integrated our LAP framework into the metagenomic analysis pipeline MetAMOS, allowing any user to reproduce quality assembly evaluations with relative ease.