Comparison of whole-genome amplification methods for next-generation sequencing of individual Onchocerca volvulus microfilariae to obtain better quality nuclear genome
PCR based whole genome amplification (WGA) was performed using 1 L of lysate from microfilariae of Onchocerca volvulus according to the manufacturer's instructions (DOPlify, PerkinElmer Inc., Shelton, Connecticut, USA). Concentrations of the WGA DNA were determined using a Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, Massachussets, USA). Sequencing libraries were constructed on samples whose DNA concentrations were above 1.0 ng/l, using Illumina DNA prep library construction kits and barcoded using unique dual indexes, according to the manufacturer's instructions (Illumina, San Diego, California, USA). An Aglient TapeStation analysis was performed on libraries using D1000 ScreenTapes (Aglient Technologies, Santa Clara, California, USA) to ensure that the libraries were within the selected size range of 400  650bp. The Qubit fluorometer was used to quantify libraries for pooling. The final 10 nM pooled library was run on a NovaSeq SP, 300 cycles.