Dear all,
FastQC has long been the standard choice for screening Illumina reads / runs. What do you use instead for Nanopore reads?
In my experience, it's always worthwhile going over the PDF report produced by MinKNOW after a run. Just like the SAV on Illumina, it gives pretty deep insight, esp. when things have gone wrong. :)
But what to use if you only have the reads? nanoQC[1] was suggested in the meeting.
From the MultiQC docs it appears that it can integrate Nanoplot output[2] (from the maker of NanoQC), which suggests NanoQC integrates in MultiQC as well. (I like MultiQC as it makes it easy to bundle QC outputs for the "customer".)
On a separate note: is there a conventional Q cutoff for reporting ONT read quality? I picked "percentage Q17+ bases" as my analogue for the typical "pct Q30+" on Illumina, because Q30 made little sense (esp. in the early Nanopore days), and Q17 corresponds to ~98% accuracy, a decent target for MinION reads. I've always wondered if there isn't a generally agreed Q-cutoff value?
Marco
[1] https://github.com/wdecoster/nanoQC [2] https://github.com/MultiQC/MultiQC/issues/1074 [3] https://github.com/wdecoster/NanoPlot