title: Illumina NOVASEQ6000 sequenced for 300 cycles
design: To prepare genomic libraries for each isolate, we used Truseq DNA Nano library preparation kits (Illumina #20015965) using  250 ng of DNA. The fragmented DNA was further end-repaired, A-tailed and ligated with unique adapters to multiplex at the sequencing stages. We measured the final quality of the library using a Qubit 4.0 fluorometer (Thermofisher #Q33238) and a DNA HS assay kit (Thermofisher #Q32851) following the manufacturers protocol. The size of the library inserts was assessed using an Tapestation 4150 (Agilent, Santa Clara, CA) and dsDNA screentape (Agilent, #50675365). Next, we diluted each library to 200 pM. Libraries were then loaded on a SP/S4 flowcell (NOVASEQ6000, Illumina) and sequenced for 300 cycles.