Which is the best tool to perform a quality trimming at 5 prime end?
I have a sample with some sequences with low quality at the the beginning (as well as at the end) and I want to trim those parts with low quality.
I believe nearly all quality-trim tools can do this (trimmomatic, BBduk, ... to name a few)
Question is if you should be doing so .....
As @lieven said all tools should do the basic quality based trimming. Some may allow you to do a windowed approach (saving some additional bases). Not sure if all tools will but bbduk can.
Cross-posted on SE