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Here's a bit of the cophylogeny at the start of the long ARG: sc2ts tree on the left
and here it is at pos 22000:
Although there are only 5 or so recombinations in the simplified ARG, on…
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Inferring a GIG from real data is probably going to be the most difficult part of the entire GIG project. This issue is to collect ideas and references.
For a start, I've just come across the paper…
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Credit to @NkRMnZr, who found this one before I did.
Description: JN.1.1/HW.1.1 (XBC.1.6.3.1.1), HW.1.1 Spike, JN.1 beginning and end.
Private mutations: Really private: C5878T, C15946C, C27635T
F…
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Hello,
Is there some way to track in which branch of the tree/lineage a given recombination break (given in -b or -f output files) occurs?
I ask because I am specifically interested in identifyi…
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Good source detailed info about types: [Vaccine Types](http://www.niaid.nih.gov/topics/vaccines/understanding/Pages/typesVaccines.aspx)
This is important information - and will require multiple types…
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There are a few tools out there that detect recombinants that might be worth adding to SARS-CoV-2. These are stolen from a slack thread with the main contributors being Bani Jolly, Wytamma Wirth, and …
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I am writing a story with lots of recombinant dialog variation. Every time I make an edit, the "story view" (right-hand panel) refreshes and shows another variant of this dialog. But this only happens…
jkant updated
8 years ago
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Hi!
Thanks a lot for this wonderful work!
My colleague did some analysis using tracer and we're a little bit confused about the output file 'cell_data.csv' and 'recombinants.txt'. It seems tha…
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For example, if we want to view all Delta + Omicron recombinants,
the standard query with pangoLEARN is: `XD* | XF* | XS* | XAW* | XAY* | XBA* | XBC*`;
the query using Nextclade to identify lineages…
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I want to write documentation about how the algorithm works (ex. [run.md](https://github.com/phac-nml/rebar/blob/main/docs/run.md)) with a case study. SARS-CoV-2 recombinant `XD` often confuses me, so…