nextclade
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nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
When using `--output-all` but not passing any value, the error message is not as helpful as it could be. I would like to know what the possible values are, printing...
Considering bug reports #908 and #907 it would probably be a good idea to have some basic CLI end-to-end testing that would catch these sorts of things and prevent regressions...
We currently have a per-sequence limit for number of displayed sequence view markers. This works well if one or a few among sequences have many markers. Users can tune the...
Here I attempt to fix https://github.com/nextstrain/nextclade/issues/903 No luck so far. Disabling `Utf8` profile and other niceties leads to ASCII-formatted table, which is equally unreadable, just with ASCII borders, instead of...
On Windows 7, in both Cmd and PowerShell, when issuing `nextclade.exe dataset list` command, it prints a table with columns not having proper spacing and with cryptic characters inside the...
I see the following in CLI help: ``` --retry-reverse-complement Retry seed matching step with a reverse complement if the first attempt failed ``` The `` should not be there I...
I tried to find out whether lz4 is supported, so I ran the following command: ``` ~/Downloads/tmp via 🅒 nextstrain ❯ nextclade run -D data -t test.tsv data/sequences.fasta -o aligned.fasta.lz4...
I've noticed that the web sequence displays stops updating after ~20 sequences are displayed. The table only updates once all sequences are analyzed, which can be quite some time if...
Right now, custom node attribute `lineage` is the only coloring that is lower cased - it would be nice if we could customize how this is shown in auspice.json, `Nextclade...
Right now, the custom node attribute is added at the very end of the coloring list - it would be nice if these came second, straight after clade
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement