Assembling Metagenomes, One Community At A Time

Abstract

Metagenomics allows unprecedented access to uncultured environmental microorganisms. The assembly of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes of dominant taxa, including uncultured members of a community. However, while numerous platforms have been developed for this critical step, there is currently no strict standard for the assembly of metagenomic sequence data. To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of eight prominent assembly tools on nine publicly-available environmental metagenomes. We found that assembler choice ultimately hinges on the scientific question at hand, the resources available and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.