Basic Package AttributesAttribute | Value |
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Title | Mason |
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Short Description | A package for the simulation of nucleotide data. |
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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. |
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Project Started | 2010 |
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Last Release | 5 years, 8 months ago |
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Homepage | http://www.seqan.de/projects/mason/ |
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Citations |
Holtgrewe, M., Mason – A Read Simulator for Second Generation Sequencing Data, Technical Report FU Berlin, June 1, 2010
[Abstract
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GSR Certification |
This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.
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Detailed AttributesAttribute Category | Attribute | Target | |
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Type of Simulated Data | Diploid DNA Sequence,
Haploid DNA Sequence,
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Variations | Single Nucleotide Variation,
Insertion and Deletion,
Inversion and Rearrangement,
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Simulation Method | Other,
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Input | |
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Data Type | Other,
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File format | Other,
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Output | |
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Data Type | Genotype or Sequence,
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Sequencing Reads | |
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File Format | Fasta or Fastq,
SAM or BAM,
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Sample Type | Random or Independent,
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Phenotype | |
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Trait Type | |
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Determinants | |
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Evolutionary Features | |
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Demographic | |
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Population Size Changes | |
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Gene Flow | |
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Spatiality | |
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Life Cycle | |
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Mating System | |
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Fecundity | |
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Natural Selection | |
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Determinant | |
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Models | |
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Recombination | |
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Mutation Models | |
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Events Allowed | |
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Other | |
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Interface | Command-line,
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Development | |
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Tested Platforms | Mac OS X,
Linux and Unix,
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Language | C or C++,
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License | BSD,
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GSR Certification | |
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No example publication using Mason has been provided.
Please
propose new citations if you are aware of publications that use this software.