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GSR: Simulator - sim3C
| Attribute | Value |
|---|---|
| Title | sim3C |
| Short Description | Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies |
| Long Description | We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error. |
| Keywords | Hi-C, Meta3C, 3C, DNA sequencing, simulation, metagenomics |
| Version | 0.2 |
| Project Started | 2017 |
| Last Release | 6 years ago |
| Homepage | https://github.com/cerebis/sim3C |
| Citations | DeMaere MZ, Darling AE, Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies., Gigascience, Feb. 1, 2018 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Dec. 9, 2022 (986 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 | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | Reference genome, |
| File format | Other, |
| Output | |
| Data Type | |
| 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 | |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used sim3C.
2022
Taylor D, Lowe R, Philippe C, Cheng KCL, Grant OA, Zabet NR, Cristofari G, Branco MR, Locus-specific chromatin profiling of evolutionarily young transposable elements., Nucleic Acids Res, April 8, 2022 [Abstract]
Ivanova V, Chernevskaya E, Vasiluev P, Ivanov A, Tolstoganov I, Shafranskaya D, Ulyantsev V, Korobeynikov A, Razin SV, Beloborodova N, et al., Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients., Front Microbiol, Feb. 3, 2022 [Abstract]
2021
DeMaere MZ, Darling AE, qc3C: Reference-free quality control for Hi-C sequencing data., PLoS Comput Biol, Oct. 11, 2021 [Abstract]