GSR: Simulator - MetaSim

Basic Package Attributes
AttributeValue
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 11 years, 7 months ago
Homepagehttps://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
Documentation
Application
Support

Last evaluated11-14-2019 (338 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
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,
Input
Data TypeAllele Frequencies,
File formatArlequin,
Output
Data TypeGenotype or Sequence, Demographic,
Sequencing Reads
File FormatGenepop,
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Carrying Capacity,
Gene FlowUser-defined Matrix,
Spatiality
Life CycleUser-Defined transition matrices,
Mating SystemRandom Mating, Age- or Stage-Specific,
FecundityInfluenced by Environment,
Natural Selection
Determinant
Models
Recombination
Mutation ModelsStepwise Mutation Model, Heterogeneity among Sites,
Events AllowedVarying Demographic Features, Change of Mating Systems,
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows, Linux and Unix,
LanguageJava,
LicenseGNU Public License,
GSR CertificationDocumentation, Application,

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]


Propose changes to this simulator