CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.

ABSTRACT:

Summary

CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. CNAsim can be used to efficiently generate single-cell copy number profiles for thousands of simulated tumor cells under a more realistic error model and a broader range of possible CNA mechanisms compared with existing simulators. The error model implemented in CNAsim accounts for the specific biases of single-cell sequencing that leads to read count fluctuation and poor resolution of CNA detection. For improved realism over existing simulators, CNAsim can (i) generate WGD, whole-chromosomal CNAs, and chromosome-arm CNAs, (ii) simulate subclonal population structure defined by the accumulation of chromosomal CNAs, and (iii) dilute the sampled cell population w

SUBMITTER: Weiner S 

PROVIDER: S-EPMC10363024 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature