Cornelius Roemer

ENH: Add Nextclade for phylogenetic informed QC

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**Is your feature request related to a problem? Please describe.** This looks like a great pipeline that includes a lot of useful tools. I've noticed that you're still adding things...

Is it intended that `,` in advanced queries behaves differently from `&`?

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Not thinking much, I used an advanced query `G2782T , T111C`. Looking at the nucleotide mutations within things matched by that query, I noticed that T111C is only present in...

I finally had a use case for the `maybe` operator so tried it out. But my queries with `maybe(T111C)` returned 0 sequences and unfortunately not even an error. So did...

When adding the `--debug` flag as in `datasets download virus genome taxon 186538 --no-progressbar --filename results/ncbi_dataset.zip --debug` the initial output (a log of HTTP requests and responses) is helpful -...

Getting error "Error: Internal error (invalid zip archive). Please try again." Take 2

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Sadly the issue is still active, at least for taxons ebola-zaire and mpox. See #356 ``` New version of client (16.16.0) available at https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-arm64/datasets. Error: Internal error (invalid zip archive)....

Lineages with potentially large deletions masquerading as stretches of Ns

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Inspired by @cassiawag's work on large deletions in ORF7/8 often masquerading as stretches of Ns in assemblies rather than as deletions, I had a look through currently submitted sequences to...

JG.3.2 sublineage defined by insertion S:212insERY (or 213RYR vs XBB ref) only [298, mostly Canada, US]

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There's a JG.3.2 sublineage in Canada that is defined by a Spike insertion S:212insERY only - there's no defining SNP compared to JG.3.2 unfortunately. GISAID query: `ins214YRR` It seems to...

DV.7.1 / XBB.1.16 recombinant (19 seqs : Canada, California)

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Breakpoint in RBD, 5' is DV.7.1, 3' is XBB.1.16 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2b165_307a70.json?s=USA/CA-HLX-STM-KT4WHJEUM/2023%7CEPI_ISL_18637220%7C ``` USA/CA-HLX-STM-KT4WHJEUM/2023|EPI_ISL_18637220|2023-11-08 Canada/ON-KHS-09109-v1/2023|EPI_ISL_18615089|2023-12-01 hCoV-19/Canada/ON-KHS-09290-v1/2023|EPI_ISL_18653743|2023-12-05 hCoV-19/Canada/ON-KHS-09425-v1/2023|EPI_ISL_18653838|2023-12-08 ``` Query: A28447G, C2227T,T28297C,A19886G ,-A2280C, -C10645T(edited)

If you add it to pypi people without brew can install it to, e.g. on Linux

One may want to synchronize saved meeting URLs between devices. To this end, one needs to know where the saved meetings are saved. I found that they are saved at...