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For CIDO, we represent the different sub-variants of SARS-CoV-2 that emerge, including the PANGO lineage identification (BA.1, BA.2, etc.). However, PANGO lineage identification gives a set of common …
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I'm not sure if this is intentional (read: I miss something that I should provide somewhere), or if this is a bug.
I tried the same thing with other SARS reads, same behavior.
### What I did:
I s…
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*Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/322
Defining mutations: FY.3.1>G4109T (ORF1a:D1282Y)>The possible branch (Usher could not show the deletion branch?…
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I wonder how many sequences are classified as "unassigned" by pangoLEARN. That is for the comparison/query between pangoLEARN and Nextclade (e.g. unassigned & nextcladePangoLineage:XAN) meaningful.
…
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Hi everyone
I have been working with the National Institute for Communicable Diseases (NICD) on some of their SARS-CoV-2 sequencing. I adapted the "variation" workflow to call variants in Illumina …
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My own analysis of Illumina (`SRR11140750`, bottom track) and nanopore (`SRR11140751`, top track) data from the same swab sample shows your variant analysis doesn't include indels:
![image](https:/…
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## Bug Report
### Affected tool(s) or class(es)
FilterAlignmentArtifact
### Affected version(s)
Docker container running 4.1.9.0
### Description
Appears to be causing a segfault
#### S…
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Hello, my name is Andrea and I am a bioinformatician who is currently working with SARS-CoV-2 sequences in order to identify quasispecies within given samples. I have been trying to use CliqueSNV so a…
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From branch 19 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.2+C832T+Orf1a:V28I,S:S31del
Query: T14700C ,C832T, C897A
No. of seqs: 26 (USA 21 Canada 1 Guatemala 1 Italy…
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From branch 21 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.4.2+Orf1a:Q575R+S:S256L,S:S31del,
Query:del21653,A1989G,C6070T
First: CLIMB-CM7YE1J6, 2024-6-26
Latest: EP…