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GSR: Simulator - SCSilicon
| Attribute | Value |
|---|---|
| Title | SCSilicon |
| Short Description | SCSilicon: a tool for synthetic single-cell DNA sequencing data generation |
| Long Description | SCSilicon efficiently generates single-cell in silicon DNA reads with minimum manual intervention. SCSilicon first creates the genome sequence (FASTA file) for each single-cell by automatically simulating a collection of genomic aberrations, including SNP, SNV, Indel, and CNV. Likewise, SCSilicon yields the ground truth of CNV segmentation breakpoints and subclone cell labels. Then, SCSilicon amplifies the genome and generates FASTQ reads. We have manually inspected a series of synthetic variations (SNP, SNV, Indel, and CNV breakpoint) generated by SCSilicon, and evaluated three start-of-the-art single-cell CNV callers. |
| Keywords | Single-cell sequencing, Simulation, Copy number variation |
| Version | 1.1.4 |
| Project Started | 2021 |
| Last Release | 3 years, 4 months ago |
| Homepage | https://github.com/xikanfeng2/SCSilicon |
| Citations | Feng X, Chen L, SCSilicon: a tool for synthetic single-cell DNA sequencing data generation., BMC Genomics, May 11, 2022 [ 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 | Diploid DNA Sequence, Haploid DNA Sequence, Single-Cell Sequencing, |
| Variations | Single Nucleotide Variation, Insertion and Deletion, CNV, |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| File Format | Fasta or Fastq, |
| 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 | |
| Development | |
| Tested Platforms | |
| Language | Python, |
| License | MIT, |
| GSR Certification | Accessibility, Documentation, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SCSilicon has been provided.
Please propose new citations if you are aware of publications that use this software.