Optimum Parameters Or Options For Shrimp Mapping

Question

[Lim]

I'm working on SOLiD colorspace data and I'm new to SHRiMP tool. I'm wondering what parameter I should set for mapping task which will not take extremely long time to finish and the quality of output is good.

For example: A 53 million reads colourspace file map against 87k bases pseudo-genome (ESTs list)

The manual of SHRiMP mentioned several parameters to use. I'm confuse what option is the best.

Answer 1

[brentp]

The defaults work very well for me. I only add the arguments to gmapper-cs

• -N for the number of threads to use and

• --single-best-mapping to report only the best alignment.

I think with that small of a reference (87KB) you don't need to split the reference so the invocation is quite simple. In my experience, even with the hg19 reference of 3GB, shrimp runs quite quickly.

I agree, there are a lot of parameters, but the defaults seem to be well tuned.