Bwa Seed Length

Question

[Bioscientist]

Just curious, anyone changes the seed length for longer reads like 100bp? Does this matter? The default is 32bp, and I used to run 36nt reads....

I would like just to use default; but hope to hear you guys' ideas. thx

Answer 1

[Chris Penkett]

There is a page here about using BWA (and other aligners) to map simulated reads by the author of BWA, the simulated reads he uses are 100 bp and he uses the default BWA parameters. The simulated reads won't have the same error characteristics as illumina reads for example, but probably most people don't play with the seed length as it should be long enough to find unique subsequences of the human genome in most cases.

Chris

[Palani Kannan]

How do we decide "long enough" seed length? Any idea or reference?