Filter reads by calculating the distribution of phred score in each individual read

Question

[Nagesh]

Dear All, I would like to know if there is any tool or script to calculate the distribution of PHRED score for each individual read and filter, if it has the high distribution low quality bases by providing cut-off value. Thanks in advance.

[Bastien Hervé]

You mean a preprocessing tool as FastQC or fastp ?

[Sej Modha]

Try FastQC - https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

[finswimmer]

Is bbduk what you are looking for?

bbduk.sh in=reads.fq out=clean.fq maq=10

This will discard reads with average quality below 10. If quality-trimming is enabled, the average quality will be calculated on the trimmed read.

[Nagesh]

By calculating the average quality, we may miss reads which are having moderate distribution of low quality bases. For example I want to retain reads which are having less than 2% bases with 20 PHRED score.

[Devon Ryan]

Fastp has an option for that. BTW, in practice base qualities tend to be fairly bimodal.

Answer 1

[Devon Ryan]

As mentioned in the comments, bbduk and fastp can both do this.