MALBACsim: A Multiple Annealing and Looping Based Amplification Cycles simulator

Single cell sequencing provides revolutionary insight into genomic heterogeneity at the molecular level. A key procedure for successful sequencing is whole genome amplification (WGA) that permits the genomic DNA of a single cell to be amplified by several orders of magnitude. A very recently reported WGA method, Multiple Annealing and Loop-Based Amplification Cycles (MALBAC), distinguished itself by providing uniformity of amplification across the genome with low amplification bias. However, MALBAC still has limitations. For example, the polymerase enzyme is prone to introduce errors and a large proportion of single-nucleotide variations are lost. The complex biological reactions involved in MALBAC are largely unaddressed and no systematic analysis for it has been reported. To reduce both the labor and costs involved in MALBAC, we have developed a computer simulation for MALBAC. By capturing several key variables, MALBAC was formulated by a mathematical model and simulated. We compared the simulated data with empirical sequencing data of Escherichia coli genomes. The experimental results demonstrated that the coverage distribution matches very well. We believe that the proposed simulator can provide both theoretical guidance and experimental cross-validation for MALBAC, thus aiding improvement of its performance.