Hi,
I am hoping to do a direct comparison of the results returned by each of bwa and shrimp. I would like to tune the parameters of bwa's aln algorithm to match the default parameters of shrimp, but I am having trouble doing so. In particular, I do not see an option for controlling the match score, and I am also not sure what kinds of limits (if any) shrimp puts on the number of gap opens/extensions. I do see that bwa's dbwtsw algorithm has a parameter for setting the match score, but the reads are 35bp each, so I am not sure if that function is the way to go. Is it possible to do what I am proposing?
Thanks!
I am hoping to do a direct comparison of the results returned by each of bwa and shrimp. I would like to tune the parameters of bwa's aln algorithm to match the default parameters of shrimp, but I am having trouble doing so. In particular, I do not see an option for controlling the match score, and I am also not sure what kinds of limits (if any) shrimp puts on the number of gap opens/extensions. I do see that bwa's dbwtsw algorithm has a parameter for setting the match score, but the reads are 35bp each, so I am not sure if that function is the way to go. Is it possible to do what I am proposing?
Thanks!
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