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- Title
CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors.
- Authors
Weiner, Samson; Bansal, Mukul S
- 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 with both normal diploid cells and pseudo-diploid cells. The software can also generate DNA-seq data for sampled cells. Availability and implementation CNAsim is written in Python and is freely available open-source from https://github.com/samsonweiner/CNAsim.
- Subjects
INTEGRATED software; CELL populations; TUMORS; PYTHON programming language
- Publication
Bioinformatics, 2023, Vol 39, Issue 7, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btad434