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Forum: Bioinformatics 12-22-2014, 09:45 AM
Replies: 3
Views: 2,265
Posted By Brian Bushnell
That's true, though note that there is also a...

That's true, though note that there is also a "reib" ("removeifeitherbad") flag which will switch the behavior between removing pairs if either fails, and removing only if both fail.

And it's also...
Forum: Bioinformatics 12-18-2014, 01:50 PM
Replies: 3
Views: 2,265
Posted By Brian Bushnell
BBDuk...

BBDuk (http://seqanswers.com/forums/showthread.php?t=42776) will do that. For example, if you want to remove phiX reads, and reads with average quality below 10:

bbduk.sh ref=phix.fasta k=31...
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