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]