Long-read metagenomic sequencing and assembly of complex microbiomes using NanoMDBG

Abstract We present nanoMDBG, an evolution of the metaMDBG HiFi assembler, designed to support kit 14, R10 ONT sequencing data through scalability and a novel pre-processing step that performs fast and accurate error correction in minimizer-space. NanoMDBG reconstructs more high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. This paradigm holds true across a range of large metagenomic ONT datasets, including a ~650 Gbp soil sample and ~250 gbp human faecal sample sequenced specifically for this study. As a result of these advances, we show that the latest ONT technology, combined with adequate long-read metagenomic library preparation, can now produce results comparable to those obtained using PacBio HiFi sequencing at equivalent sequencing depths.