SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data

摘要

Simulation software is important for developing and improving statistical methodology for next-generation sequencing data [ ]. There are currently 149 such genetic data simulators indexed by the National Cancer Institute [ ], and four of these simulators produce DNA sequencing reads with single-nucleotide variants: GemSIM [ ], NEAT [ ], SInC [ ], and CuReSim [ ]. Huang et al. [ ] proposed one of the first next-generation sequencing (NGS) simulators, but this simulator only generates bulk sequencing data. Gourlé et. al. [ ] developed a simulator specifically for metagenomic sequencing experiments. In the past year, two novel simulators for NGS DNA sequencing data have been proposed. One tool incorporates human population genetic information to simulate structural variation and different types of nucleotide variants [ ]. Another tool aims to simulate data from single-cells incorporating allelic dropout, but not false positives or different types of nucleotide variants [ ].