BBDUK and BBMERGE, which goes first

[chloe1005]

Hi,

I am trying to use MetaPhlAn2 to get a glimpse of the taxonomy composition of the shotgun data.

However, I want to do some quality control for the data. BBDUK and BBMERGE are under my consideration. May I know shall I merge first of quality trimming and filtering first?

Thanks.

[GenoMax]

I am reasonably sure that @Brian recommends merging first and then doing any trimming with bbduk.