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Would save clicks (click, ctrl+a, copy) if the tip list had a "copy to clipboard" button :)
Using this very extensively now for pango designations :)
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### Context
Just trying out `augur curate`. First painpoint is that it doesn't seem to support `zst` compressed fasta (at least according to docs).
### Description
Support zst compressed input me…
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Hello,
I was wondering if you knew of any good publicly available datasets for the V3 Artic Tiling Amplicon sequencing of hCoV-19. Ideally I would love to have a test dataset showing each of the v…
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The current nextstrain conversion script converts the "nuc" mutations, and ignores the rest. I thought that this was helpfully giving the mutations both in gene and nucleotide format - but I think now…
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Hi there, I'm getting these errors when working on non-GISAID fasta
At first, in conda env, i executed:
`samtools faidx data/bayes/covid19-refseq.fasta #the dir i cp the reference to create the f…
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## Proposed feature
Add support for one or more sequence files as input to subcommands. As we plan to support multiple inputs to `--metadata` arguments in the future, we should support multiple inp…
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*[note] This was proposed in #860, but creating this issue for discussion tailored to the de-duplication task.*
## Context
Currently, the ncov workflow has scripts for removing duplicates from
…
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We should pick between either [IANA TSVs](https://www.iana.org/assignments/media-types/text/tab-separated-values) or [RFC 4180 CSV-like TSVs](https://datatracker.ietf.org/doc/html/rfc4180) and then be…
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I already mentioned this in https://github.com/andersen-lab/ivar/issues/85#issuecomment-858686771, but I am opening its own issue because I think this is a separate problem.
There is an inconsisten…
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_Originally discussed in [Slack](https://bedfordlab.slack.com/archives/C01LCTT7JNN/p1699928691378899)_
> In [reviewing dengue ingest](https://github.com/nextstrain/dengue/pull/13#discussion_r138734…