Open hoelzer opened 1 month ago
In this context, the help mssg
--screen_reads Determines the Pangolineage of each individual read (takes time, needs --freyja and/or --lcs)
Is wrong. I am not 100% sure how LCS was doing this, but Freyja is not giving a lineage assignment for each read. Freyja is doing a deconvolution of the variant calls to estimate the proportion of lineages.
In this context, I am also wondering @DataSpott @replikation if we could not remove the screen_reads parameter?
Then, the user can just activate freyja or LCS with the parameter that is anyway available?
Alright, I tested this on patient samples.
here is the plot w/o freyja_update
which then uses a Freyja database that is part of the container (from March 2024 or so)
here is the same data and command but with freyja_update
and we can see that the update function does something (attention, the sample columns are not exactly the same)
Let's check the "interesting" samples (if I can see the colors correctly)
This works very well! And the update function also does it's job. Still, I think we should implement a more robust way where the used freyja reference db is also versionized and stored. But this can be done in another issue/PR.
In this context, the help mssg
--screen_reads Determines the Pangolineage of each individual read (takes time, needs --freyja and/or --lcs)
Is wrong. I am not 100% sure how LCS was doing this, but Freyja is not giving a lineage assignment for each read. Freyja is doing a deconvolution of the variant calls to estimate the proportion of lineages.
In this context, I am also wondering @DataSpott @replikation if we could not remove the screen_reads parameter?
Then, the user can just activate freyja or LCS with the parameter that is anyway available?
agree on this screen_reads part to simplify. but i prefer descriptions rather than tool names. (e.g. --screen_reads Uses freya to.....) maybe deprecate LCS?
Amazing results @hoelzer !
In this context, the help mssg
--screen_reads Determines the Pangolineage of each individual read (takes time, needs --freyja and/or --lcs)
Is wrong. I am not 100% sure how LCS was doing this, but Freyja is not giving a lineage assignment for each read. Freyja is doing a deconvolution of the variant calls to estimate the proportion of lineages. In this context, I am also wondering @DataSpott @replikation if we could not remove the screen_reads parameter? Then, the user can just activate freyja or LCS with the parameter that is anyway available?
agree on this screen_reads part to simplify. but i prefer descriptions rather than tool names. (e.g. --screen_reads Uses freya to.....) maybe deprecate LCA?
From my pov we could discontinue LCS. And then screen_reads would simply activate freyja.
@Krannich479 @MarieLataretu are you using LCS for anything? From my pov it's not well-updated and freyja would be anyway preferable
@Krannich479 @MarieLataretu are you using LCS for anything? From my pov it's not well-updated and freyja would be anyway preferable
We occasionally investigate the LCS results in special cases. But I agree that LCS is not up-to-date (even if we could update it)!
Maybe deprecation is a nice compromise? @replikation , it would be usable/available for some time, right?
yep
I'd vote for deprecating LCS, then. If we need LCS results in the near future for whatever reason, we'd still have the option to run it easily
Agree!
Regarding your freja
results, do you mind re-running freja if I error-correct you the read pools with herro
? This insight would bolster my (dis-)trust in EC for variant calling.
@Krannich479 pleasure.
We could also then do a re-basecalling of the run with v5 Dorado SUP and see any differences.
Freyja was recently added and also has a update parameter. To test this new functionality, we can run poreCov with a sample that has a very recent lineage assignment which is not part of the Freyja version in the container (from March I think):
Recent designations:
https://github.com/cov-lineages/pango-designation/releases/tag/v1.27
We have a Run24-123 (17.05.2024) with samples
IMSSC2-174-2024-00065 - assigned JN 1.48.1 (designated 15.04.2024) IMSSC2-99-2024-00026 - assigned JN 1.16.2 (designated 15.04.2024) IMSSC2-63-2024-00057 - assigned KP 2.3 (designated 15.04.2024)
The data is on the HPC here:
<usual-path>/2024-05-17/*Run24-123/