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GSR: Simulator - nanosim
| Attribute | Value |
|---|---|
| Title | nanosim |
| Short Description | Nanopore sequence read simulator |
| Long Description | NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. |
| Keywords | Nanopore |
| Version | 3 |
| Project Started | 2021 |
| Last Release | 8 years, 8 months ago |
| Homepage | https://github.com/bcgsc/NanoSim |
| Citations | Yang C, Chu J, Warren RL, Birol I, NanoSim: nanopore sequence read simulator based on statistical characterization., Gigascience, April 1, 2017 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | Sept. 30, 2021 (1421 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 | Genotype or Sequencing Error, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Nanopore, |
| 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 | Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| 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 nanosim.
2023
Mikalsen AJ, Zola J, Coriolis: enabling metagenomic classification on lightweight mobile devices., Bioinformatics, June 30, 2023 [Abstract]
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, et al., Systematic assessment of long-read RNA-seq methods for transcript identification and quantification., bioRxiv, July 27, 2023 [Abstract]