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GSR: Simulator - Wessim
| Attribute | Value |
|---|---|
| Title | Wessim |
| Short Description | Whole Exome Sequencing SIMulator |
| Long Description | Wessim is a simulator for a targeted resequencing as generally known as exome sequencing. Wessim basically generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation. In the targeted resequencing, we constraint the genomic regions that are used to generated DNA fragments to be only a part of the entire genome; they are usually exons and/or a few introns and untranslated regions (UTRs). |
| Version | 1.0 |
| Project Started | 2013 |
| Last Release | 10 years, 12 months ago |
| Homepage | http://sak042.github.io/Wessim/ |
| Citations | Kim S, Jeong K, Bafna V, Wessim: a whole-exome sequencing simulator based on in silico exome capture., Bioinformatics, 04-15-2013 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 06-13-2019 (1766 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, |
| Variations | |
| Simulation Method | Other, |
| Input | |
| Data Type | Other, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | |
| File Format | Fasta or Fastq, |
| Sample Type | Random or Independent, |
| Phenotype | |
| Trait Type | Binary or Qualitative, |
| Determinants | Environmental Factors, |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | |
| Gene Flow | |
| Spatiality | |
| Life Cycle | |
| Mating System | |
| Fecundity | |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | Phenogenetic, Polygenic background, |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Linux and Unix, |
| Language | Python, |
| License | Other, |
| 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 Wessim.
2020
Xing Y, Dabney AR, Li X, Wang G, Gill CA, Casola C, SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes., Front Genet, 02-21-2020 [Abstract]
Yu Z, Du F, Ban R, Zhang Y, SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles., BMC Bioinformatics, 07-23-2020 [Abstract]