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!