CellCoal 2

CellCoal: coalescent simulation of single-cell NGS genotypes

©2020 David Posada, University of Vigo, Spain http://darwin.uvigo.es

About CellCoal

CellCoal simulates the somatic evolution of single-cells. CellCoal generates a coalescent genealogy for a sample of somatic cells –no recombination– obtained from a growing population, together with a another cell as outgroup, introduces mutations along this genealogy, and produces single-cell diploid genotypes (single-nuclotide variants or SNVs). CellCoal implements multiple mutations models (0/1, DNA, infinite and finite site models, deletion, copy-neutral LOH, 30 cancer signatures) and is able to generate read counts and genotype likelihoods considering allelic dropout, sequencing and amplification error, plus doublet cells.

Getting started

1. Download: get the program from the GitHub repository at https://github.com/dapogon/cellcoal. Under the Code tab you will see a section call release. Click on it download the source code in .zip (or tar.gz) format. Then unzip the cellcoal-x.y.z.zip file (for example, cellcoal-2.0.0.zip). You should see now a folder called cellcoal-x.y.z. Move into the…