De novo species identification using 16S rRNA gene nanopore sequencing
Nanopore sequencing is rapidly emerging for microbiota-based applications. Major limitations with the current approaches are that they do not enable de novo species identification, and it is not possible to verify species assignments. This severely limits the applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-mean clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota for 3 months old infants.