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roblanf / minion_qc

Quality control for MinION sequencing data
MIT License
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Support for calibration strand data #47

Open MikeAxtell opened 5 years ago

MikeAxtell commented 5 years ago

First, off: Thanks for this great tool! It's very useful.

I have a feature request for you to consider: The current guppy basecaller has an option called '--calib_detect'. When engaged, this will detect reads that match the pre-loaded calibration strands (some lambda DNA I believe), and create several additional columns of information in the sequencing_summary.txt file. Calibration strand reads seem to be around 3.5kb in length. One great addition to your script could be one more summary plots describing the reads that were tagged as calibration strands, especially their estimated accuracy.

Cheers, Mike Axtell

roblanf commented 5 years ago

Hi Mike,

That's an excellent idea. I'm about to go on leave for a few weeks, but when I return I'll look into it.

Rob

charles-plessy commented 4 years ago

Support for basecalls ran with calib_detect would be great indeed. The simplest way would be to discard calibration reads together with the Q < 7 ones, so that the N50 of the remaining ones would reflect the contents of guppy's pass folder.