nextclade

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feat(web): show dataset machine-readable name in dataset selector

1


ivan-aksamentov

feat(web): dataset selector v2 (list version)

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ivan-aksamentov

Add sequence view pan and zoom

3

Resolves #34 It is useful, in particular, to see mutation markers that are close together. - [x] horizontal zoom and pan (horizontal scroll) in sequence view - [x] hold shift...

ivan-aksamentov

feat(web): dataset selector v2 (table version)

1

Prototype. A little broken. 

ivan-aksamentov

DO NOT MERGE: don't award matches with unknown state the full match score

1

We currently award a match `score_match` (3) and penalize a mismatch with `mismatch_penalty` (1). Ambiguous characters (`N`) match every other character and are thus always award the full score. In...

rneher

docs: broken image links on QC page

4

Example: https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/07-quality-control.html https://github.com/nextstrain/nextclade/blob/ccf2a0429e239e29a20dd4da1148b908ed2d8515/docs/user/algorithm/07-quality-control.md?plain=1#L51 gets rendered as: ```html ``` and the absolute path is not valid in the context of docs.nextstrain.org/projects/nextclade. --- However, this [Nextclade Web](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-web.html) image https://github.com/nextstrain/nextclade/blob/ccf2a0429e239e29a20dd4da1148b908ed2d8515/docs/user/nextclade-web.md?plain=1#L21 gets rendered with...

victorlin

ENH: Output reference tree attachment node into tsv/csv

1

I'm interested in seeing which regions of the tree are hot spots for attachment and which are not. To that end, it would be super nice if we output the...

corneliusroemer

When looking at non-Omicron/Delta in Nextclade through the covSpectrum integration (use [this link](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%3D2021-12-13%26variantQuery%3D%2521%2528B.1.1.529*%2B%257C%2BB.1.617.2*%2529%26downloadAsFile%3Dtrue)) I would like to be able to filter out all samples with bad QC scores specifically for...

corneliusroemer

Error using `nextclade dataset get` behind proxy: CURLE_PEER_FAILED_VERIFICATION: SSL peer certificate or SSH remote key was not OK

21

nextclade version 1.10.2 on centos-release-7-4.1708.el7.centos.x86_64 Hi, when I execute the following command, `nextclade dataset get --name sars-cov-2 --output-dir /home/[email protected]/temp/20220209/TESTNEXTLADE` I get the following error **[ERROR] Nextclade: When fetching a file...

EricFournier3

feat: sticky tooltips

1

A prototype which aims to improve user experience around tooltips. When clicked, on the aa mutation, these tooltips:  will now stick, so that information can be copied. The sticky...

ivan-aksamentov