Accuracy and completeness of long read metagenomic assemblies

Abstract

AbstractMicrobes, we can learn how microbes influence the surrounding environment, contribute to human health, and understand which pathogen interactions result in differences in disease severity. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library on the VolTRAX V2 sequence using a MinION mk1b. We basecalled using the latest version of Guppy with the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10x read depth. Polishing assemblies using Medaka had a predictable improvement in quality. Some assemblers struggled with particular members of the bacterial community, but we found Flye to be the most robust across taxa. We found Flye was the most effective assembler for recovering plasmids. Based on Flye’s consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies.