title: CHILD study: WGS of infant gut microbiome
design: Shotgun metagenomic sequencing data to an average depth of 5 million reads per sample was generated by Diversigen (Minneapolis, MN, USA) from fecal samples collected at a home visit at around 3 months (mean [SD], 3.8 [1.1] months) and a clinic visit at around 12 months (mean [SD], 12.5 [1.6] months). DNA was extracted from faecal samples using the MO Bio PowerSoil Pro with bead beating in 0.1mm glass bead plates. High-quality input DNA was verified using Quant-iT Picogreen. Libraries were then prepared and sequenced on an Illumina NextSeq using single-end 1 x 150 reads. Low quality (Q-Score < 30) and length (< 50) sequences were removed and adapter sequences trimmed. Host and low-quality reads were removed, and only samples with at least 1 million remaining reads or more were retained for downstream analysis.