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GSR: Simulator - GemSIM
| Attribute | Value |
|---|---|
| Title | GemSIM |
| Short Description | Next generation sequencing read simulator |
| Long Description | GemSIM is a software package for generating realistic simulated next generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using empirically derived error models. |
| Version | 1.6 |
| Project Started | 2013 |
| Last Release | 12 years, 6 months ago |
| Homepage | http://sourceforge.net/projects/gemsim/ |
| Citations | McElroy KE, Luciani F, Thomas T, GemSIM: general, error-model based simulator of next-generation sequencing data., BMC Genomics, Feb. 15, 2012 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | June 13, 2019 (2285 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Diploid DNA Sequence, Haploid DNA Sequence, Mitochondrial DNA, Sequencing Reads, |
| Variations | Single Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement, Genotype or Sequencing Error, Other, |
| Simulation Method | Other, |
| Input | |
| Data Type | Other, |
| File format | Other, |
| Output | |
| Data Type | Genotype or Sequence, |
| Sequencing Reads | Other, |
| File Format | Fasta or Fastq, |
| Sample Type | Other, |
| 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 | Phenogenetic, Polygenic background, |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used GemSIM.
2023
Zachariasen T, Petersen AØ, Brejnrod A, Vestergaard GA, Eklund A, Nielsen HB, Identification of representative species-specific genes for abundance measurements., Bioinform Adv, May 8, 2023 [Abstract]
2021
Tang K, Wang W, Sun Y, Zhou Y, Wang P, Guo Y, Wang X, Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment., Nucleic Acids Res, Dec. 16, 2021 [Abstract]