HTS platform comparison Illumina MiSeq data
two step-pcr approach for amplicon library generation; preparation of amplicon library for sequencing according to the manufacturer’s instructions (MiSeq Sequencing protocol); In brief, pre-dilution of amplicon pool to  2 nM and denaturation; spiking of 10 % of denatured PhiX control (Illumina, # FC-110-3001) in 6 pM amplicon pool and loading to the sample reservoir of the MiSeq Reagent Cartridge;  We used the 500-cycle v2 kit for amplicon sequencing. The run was set by using the MiSeq Control Software (MiSeq Reporter 2.2.29) according to the MiSeq System User Guide Part (# 15027617). A sample sheet (csv-file) for FASTQ format output was designed with the Illumina Experiment Manager 1.5. The run was performed for 2 x 250 bp using a paired-end approach, with automated cluster-generation, Sequencing-by-synthesis (SBS) included reversible terminator sequencing of the indexed samples, and producing demultiplexed FASTQ files.