Pacific Biosciences sequencing libraries were generated following the manufacturer's recommendations using the DNA Template Prep Kit Version 1 chemistry (Pacific Biosciences, Menlo Park, CA, USA) with the following modifications. For each sample, between 7 and 12 µg of genomic DNA was sheared to approximately 2 kb in size using a Covaris S instrument with the following parameters: temperature, 6 to 8°C; duty cycle, 20%; intensity, 0.1; cycles per burst, 1,000; time, 15 cycles × 60 seconds; shearing tubes, MiniTUBE-Clear (Covaris). DNA fragments were purified, end-repaired, and ligated with SMRTbell sequencing adapters following the manufacturer's recommendations (Pacific Biosciences) with the exception that the individual AMPure clean-up steps were purified three times rather than the recommended two. SMRTbell sequencing libraries were combined with sequencing primer and polymerase following the manufacturer's recommendations (Pacific Biosciences). The resulting complex was subjected to Pacific Biosciences sequencing, followed by primary data analysis (version 1.1.1 chemistry and analysis software) on the Pacific Biosciences RS instrument following the manufacturer's recommendations. Secondary analyses, including read filtering, were performed by SMRT Analysis versions 1.3.1 (E. coli and P. falciparum) or 1.3.0
