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Following the guide for [wastewater experimental branch]( https://gist.github.com/DrYak/e28d5d523e644ea455748d540a32ad4d). I got stuck in the last stage of vpipe deconvolution as you can see in this e…
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Big thanks to @Over-There-Is
From: https://github.com/sars-cov-2-variants/lineage-proposals/issues/2023
tr…
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Primer resplicing should be more configurable and robust to various primer naming schemes.
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Usher's placement: JN.1.1.6> G22599C(S:R346T)> C9142T> A17344G(Orf1b:I1293V), C23601A(S:S680Y)
JN.1.1.5 subbranch?
Query: A17344G, C23601A
Earliest sequence: 02-15 Songkhla, Thailand EPI_ISL_1902…
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From branch 34 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.1.1+S:S71Y,S:S31del,
Query: A24819G, del21770_21775, del21653_21655
No of seqs: 59
First: EPI_ISL_190955…
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Only SARS-CoV-2 has pango lineages per se, there's something a bit like pango for mpox, and similar (but different) systems for flu, rsv etc
Is the lineage config field required? That would not mak…
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From branch 36 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+Orf10:P10S+S:F456L
Query: T22928C,C26753T,C18894T,-G24872T,-A532G
No. of seqs: 50 (Australia 1 Brazil 34 …
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Hi all,
I inherited a setup that uses bcftools 1.8 for variant calling and decided to update to v1.17, but can no longer reproduce the (known) INDEL calls for some samples no matter how much i rela…
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The output of proper noun processing (NNP/NNPS) needs troubleshooting for the Distant Reader CORD19 project. Proper Nouns when processed and displayed should retain their capitalizations and multi-wo…