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CFSAN-Biostatistics / C-WAP

SC2 variant detection and composition pipeline
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Freyja update #21

Closed hsnguyen closed 1 year ago

hsnguyen commented 1 year ago

Hi team, Freyja newest version (1.3.12) had been released on Jan 5 while C-WAP still using 1.3.11 and I don't see freyja update from the pipeline neither. This command is to get the latest barcodes of new lineages before running freyja demix but I found the results are getting more fluctuated when the number of variables increasing now. In addition, the convergent pattern of mutations in the Omicron variant soup is making things more difficult, even collapsing results to parent lineages couldn't help, e.g. more and more BA.2.75/BA.5/ recombinant sublineages are sharing same mutations thus being messed up together.

Question:

  1. is this Freyja versioning being fixed on purpose and would stay like that for a while, i.e for the sake of consistent results somehow, or is it just a delay updating?
  2. I can see other methods for lineage demix but Freyja is the one used on genomeTrakr wastewater dashboard. Then any comment/tips on how much we can trust the results for each of these methods and Freyja there in particular?

Great works there btw, thanks.

jasmine-amir commented 1 year ago

Hello @hsnguyen and thank you for choosing C-WAP!

I am aware of the update but thank you for the extra heads up. I'd had several items due the past several weeks, so I apologize for not updating yet. I'm currently working through some compatibility fixes, and hope to push a new version out soon.

I manually run freyja update at least biweekly and pass on the lineages file to our colleague maintaining Tableau. Our most recent update was February 17, 2023. I do agree, a freyja update in prepare_envs.sh, or as a smaller, standalone script would be ideal for the upcoming C-WAP push.

Our public facing dashboard uses Freyja, wrapped within C-WAP as its only variant caller, and various other qc metrics from C-WAP too. You can read about our analysis of the other variant callers here: Kayikcioglu T, Amirzadegan J, Rand H, Tesfaldet B, Timme RE, Pettengill JB. Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples. PeerJ. 2023 Jan 26;11:e14596. doi: 10.7717/peerj.14596. PMID: 36721781; PMCID: PMC9884472..

Best, Jasmine

jasmine-amir commented 1 year ago

Closing due to inactivity