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Old 03-30-2010, 07:33 AM   #31
Location: Norway

Join Date: Aug 2008
Posts: 35

There is a setting in SOAPdenovo that I thought had some influence on this, used when you run 'SOAPdenovo contig' separately.

-M mergeLevel(default 1,min 0, max 3): the strength of merging similar sequences during contiging

However, when I experimented with different values it made no difference on the contig assembly results....not sure if it did anything with the 'consensus' base, probably not.

If you search for 'bubbles' in the Abyss, Velvet and CLC documentation you will find a lot more detail on how they deal with SNPs.
MattB is offline   Reply With Quote