Sequencing WGS and 16S amplicon libraries
Twelve WGS DNA libraries with different indices were diluted & pooled together with an equimolar concentration of each library. The pooled library was denatured and loaded on HiSEQ 2500 flow cell lanes for cluster generation in a c-Bot automated sequencing system (Illumina, Inc.), using illumina Cluster Generation kits. The sequencing was performed using TruSeq SBS v3 reagent kit (200cycles) for 100 base paired runs.
The 16S libraries were sequenced on MiSEQ platform (Illumina CA, USA). PhiX Control library was combined with the pooled V3-V4 amplicon library (expected at 20%) and loaded on to MiSEQ flow cell for clustering, to a density of approximately 570K/mm2. For sequencing MiSEQ reagent kit (500cycle) was used to generate 250 bp PE reads.