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Old 06-02-2014, 08:30 AM   #9
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707


"outd" will print every duplicate removed. So if some read has 5 copies, then 1 copy will go to "out" and 4 copies will go to "outd". Therefore I think that's what you're looking for.

By default only exact duplicates and exact containments will be removed. So if you have a 200bp contig X and a 100bp contig Y such that Y is a substring of X, then Y will be removed and will be kept. You can adjust this with the "ac" (absorb containment) flag.

Also, if the input is paired reads, they will only be removed if both reads exactly match another pair.
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