Identification of bacteriophages in vaginal swabs and cervico-vaginal secretions
Genomic DNA was extracted with Quick-DNA Fungal/Bacterial Miniprep kit (Zymo Research_. The DNA was sheared with Covaris LE220 focused ultrasonicator targeting 350 to 380bp fragments. The sheared DNA was cleaned with Agencourt AMPure XP beads. The Illumina libraries were prepared with the KAPA Hyper Prep Kit without amplification. Two AMPure clean-ups were performed after ligation and the resulting libraries were amplified with 9 cycles of PCR. A final AMPure clean-up was performed and the concentrations were quantified via an Invitrogen HS DNA Qubit and fragment sizes were analysed with an Agilent Fragment Analyzer SS.  The library construction steps were automated on the Perkin Elmer Janus platform.