Comparison of Nanopore and Illumina 16S rRNA gene amplicon sequencing. Nanopore is preferable over Illumina for 16S amplicon sequencing when species-level taxonomic classification, accurate estimation of richness, or focus on rare taxa is required

A mock community and six faecal samples were subjected to 16S rRNA gene amplicon sequencing with Nanopore GridION and Illumina NovaSeq 6000. Each sample was sequenced in three replicates with both sequencing platforms.