Cornelius Roemer
Cornelius Roemer
While it is easily possible for command line users to sample a big fasta file, users who are using the browser may not know how to do so. When one...
I was investigating what had happened in the newly designated BA.2.3.3 which appeared to have reversions at N:203/204. It turned out this is an artefact because the 3' end containing...
In most situations, users will want to automatically use the latest dataset version. Right now, that means one has to run two commands: ``` nextclade dataset get [...] nextclade run...
Currently, this is our simplest example for how to use Nextclade in our docs: ``` nextclade \ --input-fasta data/sars-cov-2/sequences.fasta \ --input-dataset data/sars-cov-2 \ --output-tsv output/nextclade.tsv \ --output-tree output/nextclade.auspice.json \ --output-dir...
It doesn't seem entirely clear to users when Pango assignments are trustworthy and when not, see https://github.com/nextstrain/nextclade/issues/760 One could for example add parentheses about the Pango assignment when the quality...
I was impatient and clicked `sort by Pango lineage` when only 100 or so sequences out of 200 had been analyzed. To my surprise, some of the sequences that hadn't...
Looking at sequences with a nucleotide deletion at `520-` ([see here](https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=https%3A%2F%2Flapis.cov-spectrum.org%2Fopen%2Fv1%2Fsample%2Ffasta%3Fhost%3DHomo%2Bsapiens%26orderBy%3Drandom%26limit%3D200%26dateFrom%3D2021-09-13%26nucMutations%3D518-%26downloadAsFile%3Dtrue)) I noticed a strange inconsistency at how we report missing nucleotides at the beginning of the sequence. Almost all...
@chaoran-chen raised that it'd be helpful to have `type` and `example` in the table documenting the `nextclade.tsv/csv` output file. This is a good idea, it's not hard to add. The...
When a gene starts or ends with Ns, a user might expect that that section of the gene is output as `X` instead of `-` as we actually do (see...
It would be nice for Nextclade web users to be able to copy mutation profiles etc. directly from the UI. Right now, this is possible only with some skill or...