RT Journal Article
SR Electronic
T1 Evaluating Metagenome Assembly on a Simple Defined Community with Many Strain Variants
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 155358
DO 10.1101/155358
A1 Sherine Awad
A1 Luiz Irber
A1 C. Titus Brown
YR 2017
UL http://biorxiv.org/content/early/2017/07/03/155358.abstract
AB 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.