Workflow parameters consisted of 100 ng DNA starting input material each of P. falciparum, E. coli, R. sphaeroides, and human, prepared independently in tubes. High molecular weight DNA was acoustically sheared to a size range of 100 to 1,000 bp using the following parameters: temperature, 6 to 8°C; duty cycle, 20% for P. falciparum and human, 1% for E. coli and R. sphaeroides; intensity, 5; cycles per burst, 200; time, 130 seconds for P. falciparum and human, 550 seconds for E. coli and R. sphaeroides; shearing tubes, MicroTubes crimpcap (Covaris, Woburn, MA, USA), using a Covaris E210 instrument. Size selection of the unamplified libraries was done with the Pippin Prep™ Instrument (SAGE Science, Beverly, MA, USA). The libraries were amplified following the protocol specifications for samples starting with 100 ng input. Final libraries were quantified and checked for size on an Agilent Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA).
