Comparative evaluation of second and third generation sequencing technologies for 16S rRNA based identification

We performed a comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies) generation sequencing technologies for 16S targeted genomics using a well-characterized reference sample (ZymoBIOMICS Microbial Community DNA Standard). Different variable regions were amplified using the Illumina MiSeq and the whole 16S rRNA gene was amplified using the MinION. Classification accuracy was determined for different workflows using different software.