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GSR: Simulator - PBSIM2
| Attribute | Value |
|---|---|
| Title | PBSIM2 |
| Short Description | a simulator for long-read sequencers with a novel generative model of quality scores |
| Long Description | PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation. |
| Keywords | PacBio |
| Last Release | 3 years, 4 months ago |
| Homepage | https://github.com/yukiteruono/pbsim2 |
| Citations | Ono Y, Asai K, Hamada M, PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores., Bioinformatics, 05-05-2021 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 10-28-2021 (898 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 | |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | |
| 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 | |
| Development | |
| Tested Platforms | |
| Language | C or C++, |
| 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 PBSIM2.
2023
Yang X, Wang X, Zou Y, Zhang S, Xia M, Fu L, Vollger MR, Chen NC, Taylor DJ, Harvey WT, et al., Characterization of large-scale genomic differences in the first complete human genome., Genome Biol, 07-04-2023 [Abstract]
Ayad LAK, Chikhi R, Pissis SP, Seedability: optimizing alignment parameters for sensitive sequence comparison., Bioinform Adv, 08-12-2023 [Abstract]