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GSR: Simulator - Grinder
| Attribute | Value |
|---|---|
| Title | Grinder |
| Short Description | Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. |
| Long Description | Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. |
| Homepage | https://sourceforge.net/projects/biogrinder/ |
| Citations | Angly FE, Willner D, Rohwer F, Hugenholtz P, Tyson GW, Grinder: a versatile amplicon and shotgun sequence simulator., Nucleic Acids Res, 07-01-2012 [ Abstract, cited in PMC ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 02-28-2023 (410 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 | Haploid DNA Sequence, RNA, |
| Variations | Single Nucleotide Variation, |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Reference genome, |
| File format | |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| 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 | |
| Language | Perl, |
| 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 Grinder.
2022
Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, et al., Design, construction, and in vivo augmentation of a complex gut microbiome., Cell, 09-15-2022 [Abstract]
McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F, Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities., Virus Evol, 10-03-2022 [Abstract]