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% N’s
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.
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% N’s
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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