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GSR: Simulator - CellCoal
| Attribute | Value |
|---|---|
| Title | CellCoal |
| Short Description | CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples |
| Long Description | 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-nucleotide 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. |
| Keywords | somatic evolution, single-cell genomics, allele dropout, amplification error, coalescent genealogy, multiple mutations models, single-cell diploid genotypes |
| Version | 1.3.1 |
| Project Started | 2019 |
| Last Release | 3 years, 6 months ago |
| Homepage | https://github.com/dapogon/cellcoal |
| Citations | Posada D, CellCoal: Coalescent Simulation of Single-Cell Sequencing Samples., Mol Biol Evol, May 1, 2020 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Sept. 30, 2022 (1080 days ago) |
| Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Single-Cell Sequencing, |
| Variations | Biallelic Marker, Single Nucleotide Variation, CNV, |
| Simulation Method | Standard Coalescent, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used CellCoal.
2022
Kang S, Borgsmüller N, Valecha M, Kuipers J, Alves JM, Prado-López S, Chantada D, Beerenwinkel N, Posada D, Szczurek E, SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data., Genome Biol, Nov. 30, 2022 [Abstract]
Gao Y, Gaither J, Chifman J, Kubatko L, A phylogenetic approach to inferring the order in which mutations arise during cancer progression., PLoS Comput Biol, Dec. 2, 2022 [Abstract]