Metagenomic shotgun sequencing: human stool samples
Briefly, the quantity of the DNA sample was measured using Picogreen                 (Invitrogen). DNA was then sheared using a Covaris and the libraries were                 constructed with the Nugen Ovation Rapid DR Multiplex System (PCR-free). The aimed                 insert size is between 400-600 bp. Amplified libraries were visualized on an Agilent                 DNA1000 chip or Caliper HiSens Bioanalyzer assay, pooled at equimolar concentrations                 and size selected using a Sage PippinPrep 2% cassette. The library pool was                 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 were demultiplexed with                 bcl2fastq.