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Old 03-30-2010, 07:22 AM   #30
natstreet
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Location: Sweden

Join Date: Nov 2009
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Quote:
Originally Posted by MattB View Post
I think overall the de novo assemblers handle SNPs quite OK (at least from my experience with CLC; Abyss and SOAPdenovo)....

Matt
Did you change any settings for ABySS or SOAPdenovo to specifically help handle SNPs or go with defaults?

Do you have any feel for how they cope with things that aren't 50:50? In a pool of individuals where you have lower frequency alleles coming from high quality reads do you know if this will cause contig splitting or is it that a consensus base will be called?
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