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Old 04-21-2010, 09:04 AM   #1
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Location: France

Join Date: Apr 2010
Posts: 3
Default BWA search strand

Hi, I am testing the bwa aligner for the first time.
I want to align short reads to the forward strand only of the human genome, but I cant find an option restricting the alignment to one strand only. It is strange, as most aligners have such an option. Did I miss it ?

I dont know the bwa algorithm in detail, but I suppose performance would be better (maybe twice as fast?) if we could align on only one strand, right?

Thanks for your answers
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