Difference between revisions of "SimSeq"
| Line 10: | Line 10: | ||
|output format=SAM alignment of simulated reads to reference | |output format=SAM alignment of simulated reads to reference | ||
|sw feature=Position and underlying base specific error model. Simulates chimeric mate-pair reads with paired-end contamination and duplicates. | |sw feature=Position and underlying base specific error model. Simulates chimeric mate-pair reads with paired-end contamination and duplicates. | ||
| − | |language=Java | + | |language=Java, C |
| − | |licence=MIT License, | + | |licence=MIT License, |
|os=All POSIX (Linux/BSD/UNIX-like OSes), | |os=All POSIX (Linux/BSD/UNIX-like OSes), | ||
}} | }} | ||
Revision as of 18:37, 4 August 2011
|
Application data |
|
| Created by | John St. John |
|---|---|
| Biological application domain(s) | Genomics |
| Principal bioinformatics method(s) | Simulation |
| Technology | Illumina |
| Created at | University of California Santa Cruz |
| Maintained? | Yes |
| Input format(s) | Fasta reference sequence |
| Output format(s) | SAM alignment of simulated reads to reference |
| 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 License |
| Operating system(s) | All POSIX (Linux/BSD/UNIX-like OSes) |
Summary: Illumina paired-end and mate-pair short read simulator. Used to sample reads from the simulated genome for the first Assemblathon.
"Error: no local variable "counter" was set." is not a number.
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
none specified
To add a reference for SimSeq, enter the PubMed ID in the field below and click 'Add'.
Search for "SimSeq" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
