title: MiSeq_wastwater_inlet
design: From each sample a targeted amplicon library was prepared. Particularly, the bacterial 16S-V4 region was amplified using dual indexed Illumina compatible primers 515f/806r as described by Kozich, et al[1]. Amplicon libraries were hen batch normalized using Invitrogen SequalPrep DNA Normalization Plates and normalized products pooled. The pools wer QC_d and quantified using a combination of Qubit dsDNA HS, Caliper LabChipGX HS DNA and Kapa Illumina Library Quantification qPCR assays and then the two combined in equimolar amounts. This final pool was loaded on an Illumina MiSeq v2 flow cell and sequencing performed in a 2x250bp paired end format using a v2 500 cycle reagent cartridge. Custom sequencing and index primers were added to appropriate wells of the reagent cartridge (515f/806r for the 16S-V4 amplicons). Base calling was done by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.0.