sequencing of evolved S. Typhimurium clone
Nextera XT libraries were prepared for each of the samples. The barcoded libraries were pooled into equimolar concentrations following manufacturers guidelines (Illumina, San Diego, CA) using the Mid-Output Kit for paired-end sequencing (2150 bp) on an Illumina NextSeq500 sequencing platform. Raw data (mean virtual coverage 361x) was demultiplexed and subsequently clipped of adapters using Trimmomatic v0.38 with default parameters8