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GSR: Simulator - MetaSim
| Attribute | Value |
|---|---|
| Title | MetaSim |
| Short Description | A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets |
| Long Description | The aim of MetaSim is to provide a tool for the simulation of reads based on given genome sequences refecting (adaptable) error models of current sequencing technologies. Additionally, the user is able to determine the abundance of the chosen taxa. Therefore, MetaSim integrates an induced tree view of the NCBI taxonomy that can be used to interactively select taxa and inner nodes of the taxonomy to con gure their relative abundances. Another feature of MetaSim allows the user to simulate an evolved population of a single genome sequence, using a population simulator. This feature is aimed at simulating the common real world situation that many di erent, but closely related strains of a lineage coexist in the same habitat. The resulting data sets can be used to plan and design metagenome studies and for evaluation and improvement of metagenomic software tools and assembly algorithms. |
| Version | V0.9.5 |
| Project Started | 2008 |
| Last Release | 15 years ago |
| Homepage | https://software-ab.informatik.uni-tuebingen.de/download/metasim/welcome.html |
| Citations | Richter DC, Ott F, Auch AF, Schmid R, Huson DH, MetaSim: a sequencing simulator for genomics and metagenomics., PLoS One, 10-08-2008 [ Abstract, cited in PMC ] |
| GSR Certification | Accessibility |
| Last evaluated | 11-14-2019 (1612 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Haploid DNA Sequence ( reads from the metagenome using a simulation of a number of different sequencing technologies), Sequencing Reads, |
| Variations | Genotype or Sequencing Error, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele Frequencies, |
| File format | Arlequin, |
| Output | |
| Data Type | Genotype or Sequence, Demographic, |
| Sequencing Reads | |
| File Format | Genepop, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Carrying Capacity, |
| Gene Flow | User-defined Matrix, |
| Spatiality | |
| Life Cycle | User-Defined transition matrices, |
| Mating System | Random Mating, Age- or Stage-Specific, |
| Fecundity | Influenced by Environment, |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | Stepwise Mutation Model, Heterogeneity among Sites, |
| Events Allowed | Varying Demographic Features, Change of Mating Systems, |
| Other | |
| Interface | Command-line, Graphical User Interface, |
| Development | |
| Tested Platforms | Windows, Linux and Unix, |
| Language | Java, |
| License | GNU Public License, |
| GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 5
The following 5 publications are selected examples of applications that used MetaSim.
2018
Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun F, Identifying <i>Group-Specific</i> Sequences for Microbial Communities Using Long <i>k</i>-mer Sequence Signatures., Front Microbiol, 05-03-2018 [Abstract]
Ai D, Pan H, Huang R, Xia LC, CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads., Genes (Basel), 06-20-2018 [Abstract]
Yao Y, Jin Z, Lee JH, An improved statistical model for taxonomic assignment of metagenomics., BMC Genet, 10-29-2018 [Abstract]
2017
Zou B, Li J, Zhou Q, Quan ZX, MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool., PLoS One, 03-28-2017 [Abstract]
Zhang SW, Jin XY, Zhang T, Gene Prediction in Metagenomic Fragments with Deep Learning., Biomed Res Int, 01-01-2017 [Abstract]