Closed hoelzer closed 2 years ago
(nextclade
also reports the frameshifts in the frameShifts
column)
(
nextclade
also reports the frameshifts in theframeShifts
color)
ah true - that we already have. ;) would be even easier than introducing another tool.
For the report I see two options:
I think, an additional column is the way to go.
@RaverJay can you add the frameShifts
column to the report, if you all agree @replikation @hoelzer ?
It's on amino acid level, but good enough for now.
@replikation following up the discussion on BC: I think it's reasonable to put a terminal print warning about Omicron sequences missing many Spike mutations and showing
sup
basecalling and/or switching to Nanopolish as options to maybe fix that.However, instead, we could also implement a general check for frameshifts (FS). For example, this could be done via https://gitlab.com/s.fuchs/covsonar in two easy steps:
All reconstructed consensus sequences can be added to a covSonar database:
Then, we can query this database via
which will give back all sequence IDs that have a frameshift.
Now, we could additionally mark them in the report and/or print a message that one should be aware of that and maybe try basecalling with a higher accuracy model or switching to Nanopolish/Medaka. Or at least investigate the sequences if the frameshift is actually true.
This would also help people w/ subsequent analyses and e,g, GISAID upload, ...
What do you think?