CellCoal: coalescent simulation of single-cell NGS genotypes
©2020 David Posada, University of Vigo, Spain http://darwin.uvigo.es
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.
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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-1.1.0.zip). You should see now a folder called cellcoal-x.y.z. Move into the folder to compile and run the program.
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Compile: type
make. The program should compile without much problem in Linux/MacOSX. A Makefile is provided for the gcc compiler. The executable file will be located in the bin folder. -
Run:
bin/cellcoal-x.y.z. In this case, the program arguments will be read from a file called parameters. Alternatively, arguments can be entered directly in the command line, or from a specific parameter file with a different name. -
Inspect results: Once the run is finished, different output files will be written by default inside a folder called results.
- If you use CellCoal, please cite: Posada D. (2020) CellCoal: coalescent simulation of single-cell sequencing samples. Molecular Biology and Evolution 37: 1535-1542. https://academic.oup.com/mbe/article/37/5/1535/5728646.