Trimming Of Illumina Rna-Seq Pe Based On Mean/Median Phred Or Richard Mott'S Algorithm

Question

[Nick]

I would like to trim my Illumina RNA-Seq PE data based on one of the following:

• mean/median PHRED score (either for the whole read or over a moving window) or
• Richard Mott's algorithm

I also would like that the program removes a read pair if after trimming one (or both) reads are cut below certain (user-defined) threshold length.

I know there are tons of trimming scripts doing some of the above. Can you point me to a script that meets both requirements (trimming and read pair removal)?

Answer 1

[bow]

Take a look at sickle, it uses a sliding-window approach (similar to Richard Mott's algorithm), allows you to define a minimum quality threshold value, and removes read pairs as well.

[Nick]

Thank you - sickle does the job. Also, it seems very fast.

Answer 2

[Istvan Albert]

A few tools are listed here Fastq Quality Control Shootout

Answer 3

[Jiacheng]

I'd recommend atria for Illumina paired-end trimming. It is a comprehensive trimmer with exceptional precision and speed.

It uses a sliding-window for quality trimming, and you can filter reads by read length:

atria --no-adapter-trim --quality-score 20 --length-range 50:500 -r r1.fastq [-R r2.fastq]