nextclade
nextclade copied to clipboard
nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
When I upload a partial genome, it is not evident in gene view that there are missing parts. It looks like the sequence is equal to reference in parts that...
It's very cool that one can use the filter to look for sequences which have a particular AA or nuc change, but it would also be cool to filter for...
@emmahodcroft noticed earlier that the run button was quite far down when one added the example sequences - the run button moves as you add files. And I just noticed...
`--output-csv` seems to be producing `;`-sep not `,`-sep The `--output-tsv` is fine. ``` % cd dattaset-dir % nextclade run --input-fasta seqiences.fasta ---dataset-dir . --output-csv out.csv % head out.csv seqName;clade;Nextclade_pango;qc.overallScore;qc.overallStatus;totalSubstitutions;totalDeletions;totalInsertions;totalFrameShifts;totalAminoacidSubstitutions;totalAminoacidDeletions;totalAmi ```
I've received a request for Avian flu datasets e.g. H5, via Twitter DM. If you'd like this feature, feel free to leave a thumbs up here to signal support.
When a site is N, rather than showing it as N in auspice.json produced by Nextclade, we give it the base of the attachment point. This threw me off when...
The clade schematic needs updating, we're using a pre-BA.4/5 version. Here's the new one: https://github.com/nextstrain/ncov-clades-schema
Maybe not surprsingly, using standalone zstd for decompression and piping into nextclade is quite a bit faster than using the packaged zstd. I guess we could add some notes somewhere...
With Beta 7, using the built-in compression is _slow_ when compressing to `xz` (using the default compression level). I'm running this in the context of a Nextstrain ncov workflow, and...
I read through the help for `--output-all` but I'm not quite sure it explains well what the argument is supposed to be. I _think_ it's the directory that we want...
Metadata
Owner
Metadata
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement