Fast tool for FASTQ Q30 calculation

Question

[emmanouil.a]

Hi, I was looking for a tool to use to calculate the number of bases with >= Q20 and Q30 in a WGS. I tested an AWK code and an R package but with a 50X WGS they need days to finish. Is there any tool that can do this work in a couple of hours? Thanks

Answer 1

[colindaven]

I use fastp for this https://github.com/OpenGene/fastp

• fast
• nice reports
• slots into multiqc
• reports Q20 and Q30 bases
• shows before and after trimming
• also works for long reads eg nanopore

[emmanouil.a]

it is great fastp and fast, but it is also performing trimming - somehow I should run fastp without performing trimming in the same time ... which means I have just to delete the trimmed fastq and keep the statistics of the original (before trimming). Great, simply.