Fig. 1

NGS reads from three different types of communities—the “balanced” community comprised of 20 unique strains of bacteria on the same order of abundance, a “staggered” community of the same 20 unique strains of bacteria with highly variable abundances, and single species communities comprised of 10 unique strains of a single species—were given as input to five different metagenomic assemblers: Omega, metaVelvet, MEGAHIT, metaSPAdes and IDBA-UD. Each assembler created contigs from the reads. By comparing the contigs generated, the ORFs called from the contigs, and the abundances of the ORFs and species, three different challenges metagenomic assemblers face were tested specifically. The results from these precise comparisons allows for a directed selection of assembler when completing a specific research goal