Mason

Basic Package Attributes
Attribute	Value
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	6 years, 6 months ago
Homepage	http://www.seqan.de/projects/mason/
Citations	Holtgrewe, M., Mason – A Read Simulator for Second Generation Sequencing Data, Technical Report FU Berlin, June 1, 2010 [Abstract ]
GSR Certification	✔Accessibility ✔Documentation Application ✔Support

Detailed Attributes
Attribute Category	Attribute
Target
Type of Simulated Data	Diploid DNA Sequence, Haploid DNA Sequence,
Variations	Single Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement,
Simulation Method	Other,
Input
Data Type	Other,
File format	Other,
Output
Data Type	Genotype or Sequence,
Sequencing Reads
File Format	Fasta or Fastq, SAM or BAM,
Sample Type	Random 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
Interface	Command-line,
Development
Tested Platforms	Mac OS X, Linux and Unix,
Language	C or C++,
License	BSD,
GSR Certification	Accessibility, Documentation, Support,