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GSR: Simulator - pIRS
| Attribute | Value |
|---|---|
| Title | pIRS |
| Short Description | Profile-based Illumina pair-end reads simulator |
| Long Description | It simulates Illumina reads with empirical Base-Calling and GC%-depth profiles trained from real re-sequencing data. It considers error & quality distributions, as well as coverage bias patterns. In addition, pIRS also comes with a tool to simulate the heterozygous diploid genomes. |
| Version | 1.11 |
| Project Started | 2012 |
| Last Release | 10 years, 5 months ago |
| Homepage | https://code.google.com/p/pirs/ |
| Citations | Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, Yue Z, et al., pIRS: Profile-based Illumina pair-end reads simulator., Bioinformatics, 06-01-2012 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 06-14-2018 (2130 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Sequencing Reads, |
| Variations | Genotype or Sequencing Error, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Saved simulation, |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| 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 | Linux and Unix, |
| Language | C or C++, Perl, |
| License | BSD, |
| 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 pIRS.
2023
Di Gregorio S, Vielma J, Haim MS, Rago L, Campos J, Kekre M, Abrudan M, Famiglietti Á, Canigia LF, Rubinstein G, et al., Genomic epidemiology of Staphylococcus aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance., Microb Genom, 05-01-2023 [Abstract]
Kuśmirek W, Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing., Sensors (Basel), 07-29-2023 [Abstract]