Question: What's the difference between Trim galore and Cutadapt when it comes to quality trimming ?
gravatar for hxlei613
4.3 years ago by
hxlei61390 wrote:


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!

cutadapt trim galore • 3.3k views
ADD COMMENTlink modified 4.2 years ago by ATpoint42k • written 4.3 years ago by hxlei61390

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.

ADD REPLYlink written 4.3 years ago by Devon Ryan97k
gravatar for ATpoint
4.2 years ago by
ATpoint42k wrote:

From trim-galore --help:

-q/--quality <int> Trim low-quality ends from reads in addition to adapter removal. For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract INT from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20.

ADD COMMENTlink written 4.2 years ago by ATpoint42k
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