title: Orientia tsutsugamushi comparative genomics and pan-genome analyses
design: Library preparations were performed using the same protocol as described in Keim et. al, 2015 with the following modifications for some samples: approximately one microgram of DNA per sample was fragmented using a Q800R2 sonicator (QSonica) with the following parameters: 3m sonication with 15s pulse on, 15s pulse off, and 20% amplitude (Keim et al., 2015). For samples that were dual-indexed, the second 8bp index oligos purchased from IDT® based on Stone et. al, 2016 (in review) were used in addition to reduce optical sequencing contamination (Stone, 2016). All samples were sequenced on an Illumina HiSeq 2000 using the 200-cycle TruSeq SBS Kit v3-HS (Illumina, Code FC-401-3001). The appropriate sequencing primers were added to the HiSeq kit as in Kozarewa and Turner, 2011 (Kozarewa & Turner, 2011).