title: 14-24_S6_R1
design: Metagenomic shotgun sequencing (NextSeq): We use Picogreen (Invitrogen) to quantitate genomic DNA samples. DNA is sheared using a Covaris and libraries are constructed with the Nugen Ovation Ultralow Library protocol. We aim for an insert size of 400 bp to maximize data. Amplified libraries are visualized on an Agilent DNA1000 chip or Caliper HiSens Bioanalyzer assay, pooled at equimolar concentrations based on these results, and size selected using a Sage PippinPrep 2% cassette. The library pool is quantified using a Kapa Biosystems qPCR library quantification protocol, then sequenced on the Illumina NextSeq in a 2x150 paired-end sequencing run using dedicated read indexing. The samples are demultiplexed with bcl2fastq.