nextclade
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nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
We are looking to extend and improve our translations. We are using `i18next` and `react-i18next` modules in the app. The extraction of English strings is performed with `yarn i18n`. The...
The presence of recombinant lineage `XA` with Alpha spike in a non-alpha background attracts Spike only Alpha sequences. Unsure how to handle this, but as a stop-gap solution we could...
I find the docker for CLI at https://hub.docker.com/r/nextstrain/nextclade, but I'd like to ask if there is any docker I can run locally to use the web interface for data analysis....
When I include an invalid nucleotide in the root sequence, all I get is a fairly non-descriptive error message: ``` [ERROR] Nextclade: Error: Invalid nucleotide: "E" ``` It'd be helpful...
If a sequence fails to align, we might reverse complement it and try again. If alignment succeeds then we have yet another informative result. We might issue a warning, to...
If and when the support for multiple visuses is added #213 we might also add an automatic detection of the virus type from sequences. This would conveniently fill the virus...
We can never be sure whether sequences with long contiguous missing fragments are what user intends to analyze or whether it is a sequencing issue that needs to be reported....
- Untranslated gene warnings are manifested in `nextclade.error.csv`, but not in main `nextclade.tsv` file. - `nextclade.tsv` file contains `errors` column, where alignment errors are manifested. - Nextclade currently does not...
Ths docs build produces a lot of warnings When running ``` make docker-docs ``` here is a relevant part of the output: ``` checking consistency... /home/user/src/docs/README.md: WARNING: document isn't included...
Thank you so much for your work on nextclade. I was wondering if code could be added so that ```--input-pcr-primers primers.csv``` could also report on if there is a deletion...
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement