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Old 08-17-2010, 01:33 PM   #7
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Location: sweden

Join Date: Sep 2009
Posts: 121

I've tested a few algorithms and the best one so far for big 454 reads has been bwa bwasw ( the long read aligner ). I would suggest though to use z = 10 or 100 if you have a big enough computer. There is another one that is highly recommended (by the maker of BWA) called Novoalign, but I haven't tried that one. BWA is easy to run, its fast and does a pretty good job as far as accuracy and specificity. It will NOT map reads smaller than 30bp, for that you have to use the bwa short aligner. Since my 454 run had reads of many sizes and in particular short reads i had to use both.
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