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GSR: Simulator - SInC
| Attribute | Value |
|---|---|
| Title | SInC |
| Short Description | An accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data |
| Long Description | An open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes. |
| Keywords | illumina |
| Project Started | 2013 |
| Last Release | 9 years, 8 months ago |
| Homepage | https://sourceforge.net/projects/sincsimulator/ |
| Citations | Pattnaik S, Gupta S, Rao AA, Panda B, SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data., BMC Bioinformatics, 02-05-2014 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | 08-09-2018 (2074 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 | Sequencing Reads, |
| Variations | Single Nucleotide Variation, Insertion and Deletion, CNV, |
| Simulation Method | Other, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Illumina, |
| 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 | Command-line, |
| Development | |
| Tested Platforms | |
| Language | C or C++, |
| License | Creative Commons, |
| GSR Certification | Accessibility, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used SInC.
2022
Wang S, Li J, Haque AKA, Zhao H, Yang L, Yuan X, svBreak: A New Approach for the Detection of Structural Variant Breakpoints Based on Convolutional Neural Network., Biomed Res Int, 03-19-2022 [Abstract]
Zhang T, Dong J, Jiang H, Zhao Z, Zhou M, Yuan T, CNV-PCC: An efficient method for detecting copy number variations from next-generation sequencing data., Front Bioeng Biotechnol, 12-01-2022 [Abstract]