Workflow: Metagenomic assembly

Assembling microbial genomes from complex metagenomic samples using long nanopore reads

Covering a vast array of applications, metagenomic sequencing allows the rapid identification and analysis of culturable microorganisms, and, importantly, has made possible the analysis of those microbes which cannot be cultured.

Compared to short-read sequencing approaches, long nanopore reads can span repeat-rich sequences — characteristic of antimicrobial resistance (AMR) genes — and structural variants. This increases the resolution of microbial classification and simplifies genome assembly, thereby providing deeper insight into the composition and function of microbial communities. With sequencing data available in real time, it is also possible to rapidly identify the species, AMR and virulence factors in a mixed microbial community.

Here we present a simple workflow for assembling microbial genomes from metagenomic samples, using MinION Flow Cells on MinION or GridION sequencing devices or PromethION Flow Cells on the PromethION 2 or PromethION 2 Solo platforms.

Download the metagenomic assembly workflow