Assessing Illumina, Nanopore and PacBio sequencing platforms at recovering high quality genomes from complex microbial communities

Cheap short-read DNA sequencing has led to a massive increase of genome reference databases, although many genome drafts from environmental systems are highly fragmented due to strain heterogeneity, micro-diversity, and repeats that cannot be resolved with short reads. This poses an issue, as the absence of genes in incomplete and fragmented genomes fails to provide important genomic information about microbial species. Here, we show that combining short reads (Illumina) with Nanopore R9 sequencing of anaerobic digester sludge enables to acquire vastly greater numbers of more complete, high quality metagenome assembled genomes, compared to a short-read-only approach (86 vs 8 high quality genome drafts). We found PacBio circular consensus sequencing to also be an effective platform for genome-centric metagenomics (74 high quality drafts), albeit at higher costs per genome draft, compared to the hybrid Illumina-Nanopore approach (59.7 vs 23.4 $ per high quality draft).