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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 | 3 years, 5 months 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 |  ✔ Accessibility |
| Last evaluated | 04-27-2021 (1082 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 | 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 | Accessibility, 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 InSilicoSeq.
2023
Tan CCS, Ko KKK, Chen H, Liu J, Loh M, SG10K_Health Consortium, Chia M, Nagarajan N, No evidence for a common blood microbiome based on a population study of 9,770 healthy humans., Nat Microbiol, 05-01-2023 [Abstract]
Harmer CJ, Nigro SJ, Hall RM, Acinetobacter baumannii GC2 Sublineage Carrying the aac(6')-Im Amikacin, Netilmicin, and Tobramycin Resistance Gene Cassette., Microbiol Spectr, 08-17-2023 [Abstract]