Assembly methods for nanopore-based metagenomic sequencing: a comparative study.

ABSTRACT: Metagenomic sequencing has allowed for the recovery of previously unexplored microbial genomes. Whereas short-read sequencing platforms often result in highly fragmented metagenomes, nanopore-based sequencers could lead to more contiguous assemblies due to their potential to generate long reads. Nevertheless, there is a lack of updated and systematic studies evaluating the performance of different assembly tools on nanopore data. In this study, we have benchmarked the ability of different assemblers to reconstruct two different commercially-available mock communities that have been sequenced using Oxford Nanopore Technologies platforms. Among the tested tools, only metaFlye, Raven, and Canu performed well in all the datasets. These tools retrieved highly contiguous genomes (or even complet

SUBMITTER: Latorre-Perez A 

PROVIDER: S-EPMC7423617 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature