We’ve released Nextclade 2.0.0 web and will the CLI v2 in the next week or two.
I’m collecting links to Threads/Changelog etc. here. Also if you have any questions feel free to ask, I’ll try to get back as soon as possible.
Announcement thread: https://twitter.com/nextstrain/status/1537481958284210177?s=20&t=zUXU6zqtjzDCXOue5DdtLQ
Further info thread: https://twitter.com/CorneliusRoemer/status/1537495606540877827?s=20&t=zUXU6zqtjzDCXOue5DdtLQ
Changelog: nextclade/CHANGELOG.md at master · nextstrain/nextclade · GitHub
Here are two additional announcements (who knows, maybe they contain the snippet of info you’ve been looking for 
)
We’ve released a rustified v2 of Nextclade (web only so far) together with 3 monkeypox datasets (all-clades, hMPXV-1, and 2022 outbreak lineage B.1)
You can already prepare CLI for v2 if you like (beta is available), we will release v2 CLI in 1-2 weeks - any testing, feedback etc. is much appreciated.
You don’t have to upgrade to v2 CLI if you don’t want to, old datasets will keep working, even new SC2 ones should for at least a month or more.
So no rush, but it could pay off and should be quite easy - CLI arguments change only slightly.
https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md
v2 is a lot faster (2-4x), can work with large genomes (like mpxv, v1 can’t!), aligns Omicron correctly (v1 struggled with Omicron 3’ end) and has a number of other convenience features.
Have a look at these two threads for some more details and check out the Changelog for a complete list.
https://twitter.com/nextstrain/status/1537481958284210177?s=20&t=zUXU6zqtjzDCXOue5DdtLQ
https://twitter.com/CorneliusRoemer/status/1537495606540877827?s=20&t=zUXU6zqtjzDCXOue5DdtLQ
If you have any questions, please comment here, I’ll try to answer all questions.
Big thanks to @Ivan Aksamentov (UniBasel/Nextstrain) who did most of the work!
Together with version 2 of Nextclade web, we have released 3 monkeypox Nextclade datasets to help with clade assignment (according to new proposed nomenclature) and sequence QC.
If you have recent sequences that are likely 2022 outbreak related, it is probably best to start with the narrowest dataset (B.1) which is the least overwhelming.
If sequences are assigned a clade of “Outgroup”, you can try a broader dataset (either hMPXV-1 or the all-clades MPXV).
You can play with the 3 datasets on clades.nextstrain.org, they are in position 2-4. There is example data available so you don’t need to get any sequences from Genbank/GISAID to try it out immediately.
The gene annotation and positions are always based on the NCBI ref sequence recently curated, so the genes are called OPG001 etc.)
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