Sliding window in Trimmomatic and PrinSeq

Question

[seta]

Hi all,

I read "Trimmomatic slides the window from the beginning (5′ end) of the read, whereas PrinSeq allows one to decide from which end the scanning should start. Note that sliding the window from the 5′ end keeps the beginning of the read until the quality falls below the threshold while sliding from the 3′ end cuts until it reaches a window with good enough quality", in a book. I'm confused with "while sliding from the 3′ end cuts until it reaches a window with good enough quality" sentence.

Could you please explain to me how sliding window work in PrinSeq?

Thanks

[Brian Bushnell]

Window-based trimming is not optimal... it's best to use the Phred algorithm, which produces optimal results (assuming the q-scores are accurate).