WGS of N. meningitidis
The Illumina reads were trimmed with Trim Galore version 0.3.7 (Babraham Bioinformatics, Cambridge, UK) to remove reads below Q28, 100 bp, and an error rate of 0.03, then mapped with bowtie version 2.1.0 (22) and used to identify base-calling errors and indels by using freebayes version 0.9.16 (https://github.com/ekg/freebayes) with base quality >20, alternate count >20, and coverage >100.