GSR: Simulator - InSilicoSeq
| Attribute | Value |
|---|---|
| Title | InSilicoSeq |
| Short Description | A sequencing simulator |
| Long Description | InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. InSilicoSeq is written in python, and use kernel density estimators to model the read quality of real sequencing data. InSilicoSeq support substitution, insertion and deletion errors. If you don't have the use for insertion and deletion error a basic error model is provided. |
| Project Started | 2017 |
| Last Release | 5 months, 1 week ago |
| Homepage | https://github.com/HadrienG/InSilicoSeq |
| Citations | Gourlé H, Karlsson-Lindsjö O, Hayer J, Bongcam-Rudloff E, Simulating Illumina metagenomic data with InSilicoSeq., Bioinformatics, 02-01-2019 [ Abstract, cited in PMC ] |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | Haploid DNA Sequence, Sequencing Reads, |
| Variations | Single Nucleotide Variation, Genotype or Sequencing Error, |
| 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 | Python, |
| License | Other, |
| GSR Certification |
No example publication using InSilicoSeq has been provided.
Please propose new citations if you are aware of publications that use this software.