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GSR: Simulator - Minnow
| Attribute | Value |
|---|---|
| Title | Minnow |
| Short Description | Minnow is a read level simulator for droplet based single cell RNA-seq data. |
| Long Description | Analysis pipelines usually validate their results by using marker genes and simulated data from gene-count-level simulators. The impact of using different read-alignment or UMI deduplication methods has not been investigated. Assessments usually start by assuming a count matrix where the effects for resolving UMI counts from raw read data are ignored. Minnow differs in the respect by modeling Unique Molecule Identifiers selection. Minnow is a read level simulator for droplet based single cell RNA-seq data. Minnow simulates reads by either sampling sequences from the de-Buijin graph of the reference transcriptome or by sampling sequences from the reference transcriptome itself. |
| Version | beta 1.3 |
| Project Started | 2019 |
| Last Release | 6 years, 7 months ago |
| Homepage | https://github.com/COMBINE-lab/minnow |
| Citations | Sarkar H, Srivastava A, Patro R, Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level., Bioinformatics, July 15, 2019 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Feb. 14, 2022 (1308 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 | RNA, |
| Variations | |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Other, |
| File format | SAM or BAM, |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | |
| 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 | C or C++, |
| License | |
| GSR Certification | 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 Minnow.
2023
Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD, DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes., bioRxiv, Aug. 17, 2023 [Abstract]
2021
Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI, Compression of quantification uncertainty for scRNA-seq counts., Bioinformatics, July 19, 2021 [Abstract]