Benchmarking State-of-the-Art Approaches for Norovirus Genome Assembly in Metagenome Sample

Abstract

A recently published article in BMCGenomics by Fuentes-Trillo et al. contains a comparison of assembly approaches of several noroviral samples via different tools and preprocessing strategies. It turned out that the study used outdated versions of tools as well as tools that were not designed for the viral assembly task. In order to improve the suboptimal assemblies, authors suggested different sophisticated preprocessing strategies that seem to make only minor contributions to the results. We have reproduced the analysis using state-of-the-art tools designed for viral assembly, and we demonstrate that tools from the SPAdes toolkit (rnaviralSPAdes and coronaSPAdes) allow one to assemble the samples from the original study into a single contig without any additional preprocessing.