GSR: Simulator - 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.|
|Last Release||7 years, 10 months ago|
|Citations||Holtgrewe, M., Mason – A Read Simulator for Second Generation Sequencing Data, Technical Report FU Berlin, 06-01-2010 [ Abstract ]|
|Type of Simulated Data||Diploid DNA Sequence, Haploid DNA Sequence,|
|Variations||Single Nucleotide Variation, Insertion and Deletion, Inversion and Rearrangement,|
|Data Type||Genotype or Sequence,|
|File Format||Fasta or Fastq, SAM or BAM,|
|Sample Type||Random or Independent,|
|Population Size Changes|
|Tested Platforms||Mac OS X, Linux and Unix,|
|Language||C or C++,|
|GSR Certification||Accessibility, Documentation, Support,|
No example publication using Mason has been provided.
Please propose new citations if you are aware of publications that use this software.