CNAsim: Improved Simulation of Single-cell Copy Number Profiles and DNA-seq Data from Tumors

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2023 Jul 14

PMID 37449891

Authors

Samson Weiner

Mukul S Bansal

Affiliations

Soon will be listed here.

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.

Citing Articles

DICE: fast and accurate distance-based reconstruction of single-cell copy number phylogenies.

Weiner S, Bansal M Life Sci Alliance. 2024; 8(3).

PMID: 39667913 PMC: 11638338. DOI: 10.26508/lsa.202402923.

Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing.

Weiner S, Li B, Nabavi S Bioinformatics. 2024; 40(8).

PMID: 39133157 PMC: 11346770. DOI: 10.1093/bioinformatics/btae506.

Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction.

Lai J, Yang Y, Liu Y, Scharpf R, Karchin R Bioinform Adv. 2024; 4(1):vbae094.

PMID: 38948008 PMC: 11213631. DOI: 10.1093/bioadv/vbae094.

Evaluation of simulation methods for tumor subclonal reconstruction.

Lai J, Liu Y, Scharpf R, Karchin R ArXiv. 2024; .

PMID: 38410652 PMC: 10896360.

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