Mason
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Application data |
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| Created by | Manuel Holtgrewe |
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| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Modelling and simulation, Sequence assembly, Mapping |
| Technology | Illumina, 454, Sanger |
| Created at | Free University of Berlin |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | FASTA, FASTQ, SAM |
| Software features | Empirical or simple model for position dependent errors, can write out sample position and extensive information about the sampled infix, haplotype simulation through mutation of reference sequence. |
| Programming language(s) | C++ |
| Software libraries | SeqAn |
| Licence | GPLv3 |
| Operating system(s) | UNIX, Windows |
| Contact: | seqan-dev@lists.fu-berlin.de |
Summary: A fast, feature-rich and hackable read simulator for the simulation of NGS and Sanger data.
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Description
We present a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes. The C++ source code is extensible, and freely available under the GPL.
Links
References
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