GSR: Simulator - Mason

Basic Package Attributes
AttributeValue
Title Mason
Short Description A package for the simulation of nucleotide data.
Long Description Mason is a package for the simulation of nucleotide data. Starting with a genome, you can simulate variants and optionally also methylation levels. From this, reads of different technologies can be simulated, optionally simulating bisulphite treatment. The variants can also be specified as a VCF file. The result are FASTQ files with the reads and optionally a SAM file with the alignment to the reference sequence. Substeps of the process are available as standalone tools, e.g. for the simulation of reads from preselected/-simulated fragments, computing of genomic sequences with variants. The time intensive part of read simulation has been parallelized.
Project Started 2010
Last Release 7 years, 4 months ago
Homepagehttp://www.seqan.de/projects/mason/
Citations Holtgrewe, M., Mason – A Read Simulator for Second Generation Sequencing Data, Technical Report FU Berlin, 06-01-2010 [ Abstract ]
GSR Certification

Accessibility
Documentation
Application
Support

Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataDiploid DNA Sequence, Haploid DNA Sequence,
VariationsSingle Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement,
Simulation MethodOther,
Input
Data TypeOther,
File formatOther,
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File FormatFasta or Fastq, SAM or BAM,
Sample TypeRandom or Independent,
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
InterfaceCommand-line,
Development
Tested PlatformsMac OS X, Linux and Unix,
LanguageC or C++,
LicenseBSD,
GSR CertificationAccessibility, Documentation, Support,

No example publication using Mason has been provided.

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