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GSR: Simulator - Mason
| 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 | 10 years, 10 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, 06-01-2010 [ Abstract ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 09-28-2022 (563 days ago) |
| 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, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used Mason.
2023
Ahmed OY, Rossi M, Gagie T, Boucher C, Langmead B, SPUMONI 2: improved classification using a pangenome index of minimizer digests., Genome Biol, 05-18-2023 [Abstract]
2021
Chen NC, Solomon B, Mun T, Iyer S, Langmead B, Reference flow: reducing reference bias using multiple population genomes., Genome Biol, 01-04-2021 [Abstract]