Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants

We evaluate the performance of three metagenome assemblers, IDBA, MetaSPAdes, and MEGAHIT, on short-read sequencing of a defined “mock” community containing 64 genomes (Shakya et al. (2013)). We update the reference metagenome for this mock community and detect several additional genomes in the read data set. We show that strain confusion results in significant loss in assembly of reference genomes that are otherwise completely present in the read data set. In agreement with previous studies, we find that MEGAHIT performs best computationally; we also show that MEGAHIT tends to recover larger portions of the strain variants than the other assemblers.