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

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.

next-gen rna-seq sequencing
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updated by Devon Ryan Devon Ryan • written by Nagesh • Nagesh

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.
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written by finswimmer finswimmer

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.

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written by Nagesh • Nagesh

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

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written by Devon Ryan Devon Ryan

1 answer

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

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written by Devon Ryan Devon Ryan

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