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Nextstrain @nextstrain
Joined September 2016
  • Tweets 2,816
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  • Followers 41,244
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Nextstrain@nextstrain
17 Nov 2025
Nextstrain is happy to announce a major update to our tuberculosis analysis, making it our first real-time (continually updated) analysis for a bacterial pathogen. Please see our new blog post for details: nextstrain.org/blog/2025-11-…

Nextstrain: New Resources for Tuberculosis

Nextstrain blog post from 2025-11-17; author(s): Kim Andrews, James Hadfield, Victor Lin, Jover Lee, Jennifer Chang

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On Oct 1, 2025, @GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
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Closing these public analyses puts the world more in the dark and concretely harms surveillance as it becomes more difficult for variant spotters to contribute to global situational awareness. 4/5
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Full blog post explaining situation and background is available here: nextstrain.org/blog/2025-11-…

Nextstrain: Interruption to GISAID-based SARS-CoV-2 sequence analyses

Nextstrain blog post from 2025-11-06; author(s): Trevor Bedford, Richard Neher and the Nextstrain team

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Nextstrain@nextstrain
20 Jun 2024
We've set up automated ingest routines to combine data from NCBI GenBank with data from the SRA. Including SRA data allows for a more up-to-date view of evolution. 2/3
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Nextstrain@nextstrain
20 Jun 2024
Phylogenetic results and resources are described in this blog post: nextstrain.org/blog/2024-06-… 3/3

Nextstrain: Phylogenetic analysis of H5N1 cattle outbreak and curated genomic data

Nextstrain blog post from 2024-06-18; author(s): Trevor Bedford, Jover Lee, James Hadfield, John Huddleston, Louise Moncla

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Nextstrain@nextstrain
20 Jun 2024
We've continued to track evolution and spread of H5N1 in cattle at nextstrain.org/avian-flu/h5n… as data has been shared by @USDA_APHIS. 1/3
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Nextstrain@nextstrain
14 Jun 2024
Thanks to work by Kim Andrews, we've recently updated our analyses and resources for measles virus. We now include automatically updated views of evolution of both the full genome at nextstrain.org/measles/genom… as well as the N450 segment at nextstrain.org/measles/N450. 1/2
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Nextstrain@nextstrain
14 Jun 2024
We also include a new Nextclade dataset to call measles genotype at clades.nextstrain.org/?datas…. This work is described on the Nextstrain blog at nextstrain.org/blog/2024-06-….
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Nextstrain@nextstrain
13 Jun 2024
We've been less active on Twitter / X for the last few months. A decent summary of recent Nextstrain activities and future directions can be seen in our annual update posted to the blog in March: nextstrain.org/blog/2024-03-…

Nextstrain: Nextstrain Annual Update March 2024

Nextstrain blog post from 2024-03-27; author(s): Nextstrain team

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Nextstrain@nextstrain
17 Jan 2024
Nextclade might be useful for many more viruses that our team can support. We therefore added the possibility of community datasets and hope that some of you will contribute datasets! We have a new tutorial to help get started: github.com/nextstrain/nextcl… 6/9

nextclade_data/docs/dataset-creation-guide.md at master · nextstrain/nextclade_data

Datasets for https://github.com/nextstrain/nextclade - nextstrain/nextclade_data

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Nextstrain@nextstrain
17 Jan 2024
This was an enormous amount of work. Congratulations to @ivan_aksamentov, @corneliusroemer and the @nextstrain team for pushing it across the finish line! 8/9
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Nextstrain@nextstrain
17 Jan 2024
We hope that this will enable many exciting applications in the future. Let us know if anything doesn’t work, what you like or don’t like, and what can be improved! Ask a question on: discussion.nextstrain.org/ Or open a Github issue: github.com/nextstrain/nextcl… 9/9

Nextstrain Discussion

Forum for Nextstrain discussion and implementation questions

discussion.nextstrain.org
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Nextstrain@nextstrain
17 Jan 2024
The seed matching step of the pairwise alignment now copes with sequences up to 15% divergence such that diverse viruses like HIV-1 can be aligned. 5/9
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Nextstrain@nextstrain
17 Jan 2024
Instead of just attaching sequences to the reference tree, Nextclade now resolves phylogenetic structure in the analyzed sequences. This makes the tree view much more informative. [Caveat: it’s a greedy tree builder that’s not a substitute for proper phylogenetics.] 3/9
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Nextstrain@nextstrain
17 Jan 2024
To facilitate discovery of datasets and guide users to the most suitable dataset, Nextclade quickly compares kmers from the input sequence to an index and highlights good matches. The CLI has a sub-command `sort` that will split input sequences into suitable subsets. 4/9
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Nextstrain@nextstrain
17 Jan 2024
With the support for splicing and slippage, we can now provide a dataset that annotates all mature proteins of SARS-CoV-2. master.clades.nextstrain.org… Going forward, this enables datasets for HIV or Hepatitis B virus. 2/9
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Nextstrain@nextstrain
17 Jan 2024
After many months of work, we are releasing Nextclade v3 with major changes: - Splicing, slippage, and circular genomes - Local tree-building - Auto-suggestion of suitable datasets - Align more divergent sequences - Community datasets clades.nextstrain.org (desktop only) 1/9
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