SimSeq

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
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

• SimSeq Homepage [ edit link ]

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References

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