Vaginal metagenome of Homo sapiens
Bacterial DNA extraction DNA was extracted using the ZymoBIOMICS kit (D4302, Zymo Research, USA) according to the manufacturers instructions. Library preparation and sequencing DNA was used to prepare a Nextera XT sequencing library (Illumina), according to the suppliers protocol (Document # 15031942 v06). The  library was sequenced on a NovaSeq 6000 instrument with paired-end 150 nt sequencing protocol. FASTQ read sequence files were generated using bcl2-convert version  4.2.4 (Illumina). Initial quality assessment was based on data passing the Illumina Chastity filtering.  Subsequently, reads containing Phix control signal were removed using Bowtie2 version 2.4.5 (Langmead et al., 2012). In addition, reads containing (partial) adapters  were clipped (until a minimum length of 50 bases) using fastp version 0.23.4 (Chen et al., 2018). The second quality assessment was based on the  remaining reads  using FASTQC quality control tool version 0.11.9. Illumina data was randomly subsampled to a maximum of 550 Mb data using the reformat tool in BBmap version 38.46 (Bushnell, 2014).
SUB15346123
Flater_metagenome