Short sequences are flagged with a QC pass about nextclade HOT 4 CLOSED

the main issue should be solved. but QC for short sequences is not adequately addressed. We are looking into a better organization of the QC procedure, so will hopefully tackle this along with it.

from nextclade.

Thanks a lot @george-githinji, very good points!

we didn't think about partial sequences when doing QC or calling clades -- I'll address this ASAP.

from nextclade.

I don't view missing 5' and 3' parts as a QC issue. It likely means only a fragment was sequenced. But the QC criteria should be scaled relative to length of the fragment. Let us know how you'd expect the app to behave.

from nextclade.

One approach might be to disregard Ns within the 3' and 5' regions. This implies identifying these regions from a submitted sequence.

from nextclade.