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Old 04-07-2010, 07:53 AM   #5
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by Chipper View Post
BWA uses the -n parameter for the number of mismatches in the full read (-k is for the seed). Bowtie uses -n for the seed and then allows any # of mismatches in the 3' end. And then BFAST uses -n for the number of threads. Wouldn't it be great if these parameters were standardized...?
You absolutely right about BWA "-n", that is my error.

As for standardizing the options, that would be lovely (BFAST came out in mid/early 2008, look how many aligners there are now), but the differences in the algorithm are too substantial in my opinion. For example BWA and other BWT algorithms search (exponentially) over a certain # of mismatches/differences, while BFAST and spaced seed (index/hash) algorithms do not necessarily guarantee to find up to a certain # of mismatches (say 99% of reads with k # of mismatches). Therefore, there can be a parameter "up to k mismatches" in the former but not in the later.

Remember these software are usually written by graduate students (who need to graduate) or post-docs. Maybe a faculty position () would allow us to give better support and standardization.
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