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I think that a | as a separator may cause problems during upload to GISAID.
Under "Specimen source" in the export, can we have a comma separate the parts?
 distinct variants:
(1) Variant with the following mutations in the spike protein: H69-/V70- | Y144- | N501Y | A570- | -57…
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Hi,
I have identified a new variant with the following mutations in the spike protein: H69-/V70- | Y144- | N501Y | A570- | -572D | D614G | P681H | T716I | S982A | D1118H | D1199V (GISAID IDs: EPI_I…
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Dear,
I have a bunch of sequences that are presumably wrongly assigned to lineage B.1.177, while they should be classified to the lineage B.1.525 (or sublineages).
These samples share all the ca…
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Switched to a multiple input setup recently. Followed the example file. This is with nextstrain software up to date and files pulled from github last week. Aborted runs normally can be 'unlocked' with…
mbosm updated
3 years ago
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Hi,
I was trying to run the nextstrain to align and generate a tree for a list of fasta nucleotide sequences coming from a targeted sequence of the S gene.
I have update the build.yaml to lower in…
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At PHE we currently use jclusterfunk annotations to track clusters within the large phylogenetic tree published by COG. For the most part the clusters are as expected, however we do find edge cases. I…
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Copy select files into a deliverables folder to streamline deliverables to Helix and for GISAID upload
Helix wants: untrimmed bams, consensus sequences and summary csv plus lineages.
GISAID wa…
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-Depends on communication with Shashank for Inspect
-Depends on communication with Andersen lab for upload requirements
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by Katherine Laiton-Donato, Carlos Franco-Muñoz, Diego A. Álvarez-Díaz, Héctor Alejandro Ruiz-Moreno, José A. Usme-Ciro, Jhonnatan Reales-González, Diego Andrés Prada, Sheryll Corchuelo, Maria T. Herr…