M22249_neisseria_meningitidis
Illumina sequencing libraries were prepared from extracted DNA by first shearing it to 600 bp using a Covaris LE220 focused ultrasonicator (Covaris, Inc., Woburn, MA). The sheared DNA was processed with the NEBNext ultra DNA library preparation kit following the manufacturers protocol (New England Biolabs, Ipswich, MA), using dual barcoding indices. Reads were trimmed using Cutadapt 1.8.1. (16) to remove adapter sequences and bases with a quality score of <Q20, and assembled with SPAdes v3.7 (17). Genomes were required to have an average coverage depth of 25x, and contigs were excluded as spurious if they had 10% of the genome-wide coverage depth.