Generalise to other viruses - added customisable reference sequence and outgroup to config file#166
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mattarnoldbio wants to merge 1 commit into
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Generalise to other viruses - added customisable reference sequence and outgroup to config file#166mattarnoldbio wants to merge 1 commit into
mattarnoldbio wants to merge 1 commit into
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Hi Aine!
Off the back of our conversation (semi-)recently, here are the changes I made to Civet to generalise outside of the SARS-CoV2 context. Seems like it was just the ingestion of outgroup/reference sequences that needed changing in the actual code. From memory, the minimum sequence length and trim parameters (unsurprisingly) need to be specified explicitly in the config for non-SARS-CoV2 use cases.
I'll attach a zip archive of all the data (test and background data, config file, outgroup, reference) needed to run on the example I used to test this, piscine myocarditis virus (PMCV) so you can satisfy yourself it is working as you would hope.
example.zip
Let me know if you need anything else.
P.s. Just in case it's useful, here's the SOP I wrote for grant partners:
CIVET_ClusterAnalysisSOP.docx