SimSeq
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Application data |
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| Created by | John St. John |
|---|---|
| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Modelling and simulation |
| Technology | Illumina |
| Created at | University of California Santa Cruz |
| Maintained? | Yes |
| Input format(s) | FASTA |
| Output format(s) | SAM |
| Software features | Position and underlying base specific error model. Simulates chimeric mate-pair reads with paired-end contamination and duplicates. |
| Programming language(s) | Java, C |
| Licence | MIT |
| Operating system(s) | POSIX |
Summary: Illumina paired-end and mate-pair short read simulator. Used to sample reads from the simulated genome for the first Assemblathon.
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Description
Samples either paired-end or mate-pair style short reads simulating what you would get from an Illumina run. Both paired-end and mate-pair methods allow you to simulate duplicate reads, while the mate-pair method also simulates chimeric reads, and paired-end contamination. The program also utilizes a position and reference base specific error model to simulate error.
Links
References
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| Web Search | Wiki Sites | Scientific |
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