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Old 09-23-2014, 10:55 PM   #1
fahmida
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Location: Australia

Join Date: Aug 2010
Posts: 54
Default Multiple read QC steps (trimming, filtering etc) in one go ... what's the best way?

Hi,

I know there are many versatile tools (bbduck, trimmomatic etc. to name a a few) that can trim low quality bases, adapters etc. I wonder what would be the best way to do the followings with a single command or pipeline:
1) Adapter/Quality Trimming and Filtering
2) removing reads with greater than 5% Nís
3) removing reads where 20% or more of the calls were considered low quality bases
4) removing duplicated reads
If still I am not asking for too much, perhaps :-)
5) error correcting reads as well!

Thanks.
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