WGS of E. coli WT culture flask experimental population 2
Library preparation and metagenomic sequencing were performed at the Vanderbilt University Medical Center. The samples were normalized to target 100 ng of total input for each sample, and libraries were prepared using the Twist Biosciences kit (Twist, 104207) following a miniaturized version of the manufacturers protocol. The libraries were quantitated and pooled for downstream processing. The pool quality is assessed using the Agilent Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (Kapa, KK4873) and the QuantStudio 12K instrument. Prepared libraries were pooled in equimolar ratios, and the resulting pool was subjected to cluster generation using the NovaSeq 6000 System, following the manufacturers protocols. 150 bp paired-end sequencing was performed on the NovaSeq 6000 platform targeting 2M reads per library. Raw sequencing data (FASTQ files) obtained from the NovaSeq 6000 was subjected to quality control analysis, including read quality assessment. Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.