GSR: Simulator - MetaSim

Basic Package Attributes
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 12 years, 6 months ago
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


Last evaluated11-14-2019 (658 days ago)
Detailed Attributes
Attribute CategoryAttribute
Type of Simulated DataHaploid DNA Sequence ( reads from the metagenome using a simulation of a number of different sequencing technologies), Sequencing Reads,
VariationsGenotype or Sequencing Error,
Simulation MethodForward-time,
Data TypeAllele Frequencies,
File formatArlequin,
Data TypeGenotype or Sequence, Demographic,
Sequencing Reads
File FormatGenepop,
Sample Type
Trait Type
Evolutionary Features
Population Size ChangesConstant Size, Carrying Capacity,
Gene FlowUser-defined Matrix,
Life CycleUser-Defined transition matrices,
Mating SystemRandom Mating, Age- or Stage-Specific,
FecundityInfluenced by Environment,
Natural Selection
Mutation ModelsStepwise Mutation Model, Heterogeneity among Sites,
Events AllowedVarying Demographic Features, Change of Mating Systems,
InterfaceCommand-line, Graphical User Interface,
Tested PlatformsWindows, Linux and Unix,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

The following 5 publications are selected examples of applications that used MetaSim.


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]


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]

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