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 complete genomes) directly from the metagenomic data. Despite the intrinsic high error of nanopore sequencing, final assemblies reached high accuracy (~ 99.5 to 99.8% of consensus accuracy). Polishing strategies demonstrated to be necessary for reducing the number of indels, and this had an impact on the prediction of biosynthetic gene clusters. Correction with high quality short reads did not always result in higher quality draft assemblies. Overall, nanopore metagenomic sequencing data-adapted to MinION’s current output-proved sufficient for assembling and characterizing low-complexity microbial communities.
Highlights
Metagenomic sequencing has revolutionized the way we study and characterize microbial communities
This work demonstrates the suitability of using nanopore sequencing exclusively for assembling low-complexity microbial communities, and paves the way towards the standardization of bioinformatic pipelines for long-read sequencing data
The data released by Nicholls et al.[15] was used in order to study the suitability of nanopore sequencing to characterize low complex microbial communities
Summary
Metagenomic sequencing has revolutionized the way we study and characterize microbial communities. When performing de novo assemblies, Illumina sequences often result in highly fragmented genomes, even when sequencing pure cultures[8,9]. This is a consequence of the inability to correctly assemble genomic regions containing repetitive elements that are longer than the read length[9]. This fragmentation problem is magnified when handling metagenomic sequences due to the existence of intergenomic repeats that are shared by more than one taxon present in the microbial c ommunity[10]. It has to be noted that microbial communities often contain related species or sub-species in different-and unknown- abundances, resulting in extensive intergenomic overlaps that can hinder the assembly p rocess[11,12]
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