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Hi,
We submitted a set of SARS-Cov2 assembled genomes to the Nextclade web interface, it assigned these samples to clade 20H/501Y.V2. However, when we downloaded the report file in the csv format w…
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Keeping track of those entries removed (where and why).
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Gisaid curator noticed many 1bp frameshift deletions in the consensus sequences.
Also the pipeline misses a homopolymer correction (position 11028)
List of potential artefacts:
Mutation | Aminoac…
BVeer updated
3 years ago
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**Proposal for new-sublineages AY.13-AY.22 within B.1.617.2**
by Chris Ruis
**Description**
Examination of the latest UShER tree showed multiple cases of introduction of B.1.617.2 into specific c…
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Hi Hyun-Hwan Jeong,
I've tried using SalmonTE on some penguin data from our lab, but i'm having issues with the index step.
I created my FASTA file of repeat sequences
[EmperorTranscrNew_familie…
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**Proposal for 7 new sub-lineages within B.1.1.318**
by Chris Ruis
**Description**
Sub-lineages of B.1.1.318
Examination of the B.1.1.318 clade in the latest UShER tree shows six instances of im…
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Hello,
I am moving from StrainPhlAn2 to StrainPhlAn3, and one question is whether flag --clade in StrainPhlAn3 is mandatory or not? If yes, and I want to investigate all clades without defining spe…
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Hi,
I am trying to use CCMgen with a tree inferred by [fasttree2](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009490).
Two problems :
1)
The "intermediate" clade…
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I want to be able to manually assign colours once based on species/population and once based on clades, I tried this for 64 tips:
`colours(tree$tip.label)
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## B.1.617.2 sub-lineage with ORF1a: I3731V
Zach Hensel
### Description
**Sub-lineage of**: B.1.617.2
**Earliest sequence**: 23 April, 2021 Illinois, USA (searched for N:G215C, ORF1a:T3646A, ORF…