Fast tool for FASTQ Q30 calculation
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8 weeks ago
emmanouil.a ▴ 120

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

Q30 FASTQ Q20 • 349 views
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Entering edit mode
8 weeks ago

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
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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.

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