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GSR: Simulator - SimLoRD
| Attribute | Value |
|---|---|
| Title | SimLoRD |
| Short Description | SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. |
| Long Description | SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. |
| Version | 1.0.4 |
| Project Started | 2016 |
| Last Release | 5 years, 7 months ago |
| Homepage | https://bitbucket.org/genomeinformatics/simlord/src/master/ |
| Citations | Stöcker BK, Köster J, Rahmann S, SimLoRD: Simulation of Long Read Data., Bioinformatics, Sept. 1, 2016 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | June 22, 2021 (1521 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 | |
| Simulation Method | |
| Input | |
| Data Type | Other, |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Illumina, Roche 454, SOLiD, IonTorrent, PacBio, Nanopore, Other, |
| 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 | Windows, Mac OS X, Linux and Unix, |
| Language | Python, |
| License | MIT, |
| 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 SimLoRD.
2023
Wang X, Huang M, Budowle B, Ge J, TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads., Front Genet, July 18, 2023 [Abstract]
2022
Lesack K, Mariene GM, Andersen EC, Wasmuth JD, Different structural variant prediction tools yield considerably different results in Caenorhabditis elegans., PLoS One, Dec. 30, 2022 [Abstract]