Sequel sequencing
PacBio libraries were produced using the SMRTbell Template Prep Kit 1.0 according to manufacturers instructions. In brief, 500 ng of DNA (amplicon pool) was purified using  PB AMPure beads before DNA damage repair and end-repair followed by ligation of hair-pin adaptors to generate a SMRTbell library for circular consensus sequencing. The library was then subjected to exo treatment and PB AMPure bead wash for clean-up. Each 384-plex library was sequenced in a single SMRTcell 1M for the PacBio Sequel I instrument using a Sequel 3.0 polymerase and 480 minute movie time, allowing for approx. 32 passes of the polymerase on the barcoded msp1, msp2, glurp and csp products (16 passes on the positive strand + 16 passes on the negative strand). CCS reads were assigned to individual samples and primers were computationally trimmed using the Lima package (in asymmetric mode) that is included in the SMRT Link toolbox (version 10.0.0.108728)