Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.

ABSTRACT:

Background

Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available softwa

SUBMITTER: Gerner SM 

PROVIDER: S-EPMC6889603 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature