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]