Comments (1)
Hi Laura @laura-bankers,
Thanks for your interest! We are very happy that people are reaching out and asking about new pathogens.
Do you mean these files?
https://github.com/nextstrain/nextclade/tree/master/data/enterovirus/d68
Sadly, these are only a genome annotation, a reference sequence and a few example sequences, so they are not enough to run Nextclade (which also currently requires a reference tree, QC config and virus properties config). These files are historically only there to provide some examples to run Nextalign (which is like Nextclade, but only does alignment and translation).
Or maybe you've seen other files somewhere else? Could you please send me a link?
I don't exclude a possibility that there are datasets exist on the internet, created by the community and which we don't know about.
A few notes which may help you in your work with Nextclade:
Dockstore containers is not something Nextclade team is aware of. This is not an official source. Probably some community effort. Which we are happy to hear about, but don't have bandwidth to support officially.
Official docker containers (on DockerHub) or any other official means of distribution of Nextclade CLI (listed in the docs) don't contain datasets on purpose. Nextclade is pathogen-agnostic by design. It only reads an index.json file hosted elsewhere on our servers, which contains a list of known datasets, and then can download datasets from this list from our server using nextclade dataset get
command. This is purely for convenience. But you can also load any dataset you want from your computer. So, if you found a dataset you like, or created one, you can just pass it into Nextclade as you would do with an officially downloaded one.
You can try and build your own dataset to support a new pathogen. It's quite a challenging adventure at the time. But I gathered some of the information in response to this issue in hope that it helps people: #1225
We are working on the next major version of Nextclade - version 3. In the new version there will be significant changes to datasets. Nextalign will be removed and all dataset files previously required for Nextclade will become optional - this way you could build a dataset gradually, starting small and adding new features later as needed. And we are also hoping to document creation of new datasets better and t provide tools to make the process easier. It's all coming soon. Stay tuned!
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Related Issues (20)
- Include aligned sequences and translations in ndjson
- ENH(nextalign cli): show default values in --help usage statement HOT 4
- Maximum Sequence Limit? HOT 2
- Web: Grey scale coloring for region/country/divison if scale not predefined in reference tree HOT 5
- How to decide if the reversionSubstitutions are valid variants or not and whether to keep them? HOT 2
- Direct Auspice SVG Download
- ENH: enlarge Visualization when more nucleotides/Codons even if mutations not fall in striclty adjacent codons but close enough to need a whole view. HOT 2
- Updating certain parts of the JSON file output from Map to Array HOT 2
- linux-musl artefact gets slower rather than faster when parallelizing in contrast to gnu HOT 5
- Parsing PCR primers HOT 2
- how many SARS-COV-2 sequences can nextclade handle in a MSA file? HOT 8
- Is there any example for handling HIV data? HOT 2
- Web crash: The target <seqName> could not be identified in the dom HOT 2
- Show "browser not supported HOT 1
- Show "browser not supported" modal only once per session HOT 3
- if the qc.overallStatus of my sequences are mediocre, can we keep them for next step analysis? HOT 5
- web-based nextclade issue when using another reference HOT 8
- web(minor): when customizing dataset files, it always says "pasted sequences" even if the field is for tree HOT 2
- I upload 1490 sequences to nextclade, and upload to auspice.us, why it shows me 4255 sequences? HOT 2
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