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GSR: Simulator - PaSS
| Attribute | Value |
|---|---|
| Title | PaSS |
| Short Description | PaSS is an effective sequence simulator for PacBio sequencing |
| Long Description | PacBio Sequencing Simulator (PaSS) can learn sequence patterns from PacBio sequencing data currently available. In addition to the distribution of read lengths and error rates, we included a context-specific sequencing error model. Compared to existing PacBio sequencing simulators such as PBSIM, LongISLND and NPBSS, PaSS performed better in many aspects. Assembly tests also suggest that reads simulated by PaSS are the most similar to experimental sequencing data. |
| Keywords | PacBio |
| Project Started | 2019 |
| Last Release | 6 years, 2 months ago |
| Homepage | https://cgm.sjtu.edu.cn/PaSS/ |
| Citations | Zhang W, Jia B, Wei C, PaSS: a sequencing simulator for PacBio sequencing., BMC Bioinformatics, June 21, 2019 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | Oct. 28, 2021 (1393 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 | Single Nucleotide Variation, Insertion and Deletion, CNV, Genotype or Sequencing Error, |
| Simulation Method | Resample Existing Data, |
| 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++, Perl, |
| License | |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used PaSS.
2022
Shaw J, Yu YW, flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning., J Comput Biol, Feb. 1, 2022 [Abstract]
Logan R, Fleischmann Z, Annis S, Wehe AW, Tilly JL, Woods DC, Khrapko K, 3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data., BMC Bioinformatics, March 20, 2022 [Abstract]