What's the difference between Trim galore and Cutadapt when it comes to quality trimming ?

Question

[hxlei613]

Hi.

Trim galore makes use of cutadapt. Both of them use the algorithm thar is the same as the one used by BWA. However, in cutadapt only the 3’ end of each read is quality-trimmed by default. It can trim the 5’end as well if you want. I wonder wether Trim galore performs quality trimming only on 3'end or 5'and 3'end ?

Thank you very much!

[Devon Ryan]

Trim Galore is just a perl script, have you looked inside it for the exact cutadapt command it's using? Just search for path_to_cutadapt.