3.9.1

Nextclade 3.9.1

Fix: clade mismatch between placed node and parent node

This version addresses an issue when sometimes clade (or clade-like attribute, such as lineage) of the placed query node might not always match the clade of its parent.

The query node placement is adjusted during the greedy tree building, and sometimes the branch needs to be split and a new auxiliary internal node to be inserted to accommodate the new node. Previously, Nextclade would copy the clade of this internal node from the attachment target node. However, this is not always correct and can lead to mismatch between clade of the query node and of the new internal node.

In this version we added a voting mechanism, which calculates a mode of the clades involved: of the parent, target and query nodes. The same procedure is repeated for each clade-like attribute. After that, in some cases, branch labels also need to adjust their positions.

This should not change the clade assignment for query samples, but only the clades of the inserted auxiliary internal nodes, to make sure that the tree is consistent.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.9.0

Nextclade 3.9.0

Nextclade CLI: Obtain CA certificates from platform trust store; add NEXTCLADE_EXTRA_CA_CERTS / --extra-ca-certs

Nextclade CLI users have previously reported issues with CA certificates when fetching datasets from an organization's network (e.g. in a university or in a company).

Starting with this version, Nextclade CLI respects the OS-level trust store configurations. This includes private CAs and self-signed certificates. Ensures backward compatibility and functionality across different platforms, including those lacking a native trust store or with outdated ones.

We introduced a NEXTCLADE_EXTRA_CA_CERTS environment variable and --extra-ca-certs option which allow adding additional CA certificates to the trust store specifically for Nextclade, for when modifying the system's trust store isn't desirable/possible. See #1536 for more details.

Update Auspice tree visualization to 2.58.0

Auspice tree visualization package has been updated from 2.56.0 to 2.58.0. See Auspice changelog here.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.8.2

Nextclade 3.8.2

Fix detection of number of threads in Nextclade Web

Sometimes Nextclade Web would detect incorrect number of available CPU threads and would create too many processing threads. This could cause additional overhead and slowdown the runs. We observed this behavior in non-chromium based browsers, such as Firefox and Safari. This has been fixed now. The number of threads has been clamped to 3 by default. You can modify this in "Settings" dialog.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.8.1

Nextclade 3.8.1

Fix crash when using column config

Since 3.8.0, Nextclade could crash when particular combinations of CSV/TSV columns selected in "Column config" tab on "Export" page in Nextclade Web or with --output-columns-selection argument in Nextclade CLI. This has been resolved.

Remove extra spaces in ref node selector

Remove extra spaces in the text of entries in the "Relative to" dropdown selector in Nextclade Web.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.8.0

Nextclade 3.8.0

Relative mutations

Nextclade now calls mutations relative to multiple targets. Additionally to previously available mutations relative to reference and mutations relative to parent tree node (private mutations), Nextclade now calls mutations relative to clade founder tree nodes, and relative to custom nodes of interest if defined in the dataset (e.g. vaccine strains).

Nextclade Web now has an additional dropdown selector for the target of mutation calling. Output files has new columns/fields for mutations relative to clade founders (founderMuts) as well as for mutations relative to custom nodes (relativeMutations).

See documentation for more details.

Update Auspice tree visualization to 2.56.0

Auspice tree visualization package has been updated from 2.55.0 to 2.56.0. See Auspice changelog here.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.7.4

Nextclade 3.7.4

Nextclade Web

Upgrade Auspice to 2.55.0, add polyfills

This definitively resolves crash due to missing JavaScript polyfills, which occurred in Nextclade Web 3.7.2

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.7.3

Nextclade 3.7.3

Nextclade Web

Fix crash on tree page in Nextclade Web

Temporarily downgrade Auspice from 2.55.0 to 2.54.3 to prevent the tree page in Nextclade Web from crashing. The definitive fix will follow.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.7.2

Nextclade 3.7.2

General

[fix] Avoid duplicate node names in the output Auspice JSON tree

When multiple query samples were to be placed onto the same node on the reference tree, sometimes multiple auxiliary nodes could be created having the same name. Node names are expected to be unique for Auspice visualization to work correctly, so when visualizing the tree Auspice have been renaming these nodes and emitting warnings into browsers' dev console.

In this version we pick unique names for the auxiliary nodes during placement, so that there are no more warnings. Users may observe changes in some of the node names when inspecting output Auspice JSON file. However, this unlikely to affect most users' work.

Nextclade Web

[fix] Ensure dataset "updated at" date is displayed in Nextclade Web

Since 3.7.0 Nextclade Web is not showing "updated at" date for any datasets. This has been fixed.

[fix] Ensure frame shift and insertion markers in sequence views can also be toggled

Most markers can be toggled on or off on the sequence views in "Settings" page in Nextclade Web, however frame shifts and insertions could not be. We added the missing toggles.

[fix] Correctly style details/summary component

The text in details/summary ("collapse", "spoiler") component (e.g. the list of SC2 lineages) overflowing and producing garbled text in dataset readmes and changelogs. This has been fixed.

[dep] Update Auspice tree visualization to 2.55.0

Auspice tree visualization package has been updated from 2.53.0 to 2.55.0. See Auspice changelog here.

Internal

[infra] Fix feature-policy and permission-policy HTTP headers

The deprecated feature-policy header was removed entirely and interest-cohort entry was removed from the permission-policy header. Latest versions of web browsers should no longer emit warnings into console.

[test] Test Nextclade CLI on more Linx distros

Additionally to the previous, we now test Nextclade CLI on the following newer Linux distributions:

• Amazon Linux 2.0.2024
• Debian 12
• Fedora 41
• Oracle Linux 8.9
• Ubuntu 24.04

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.7.1

Nextclade 3.7.1

Warn if reference sequence does not match root sequence of the tree

When both a standalone reference sequence and Auspice tree containing .root.sequence.nuc are present, Nextclade will check that these are the same sequence. If not, a warning is emitted to stderr for Nextclade CLI and to browser's dev console for Nextclade Web. This is mostly useful for dataset authors, for debugging.

Fix error when selecting a CDS in genome annotation visualization in Nextclade Web

Nextclade sometimes displayed an error in the peptide view when switching CDS by clicking on annotation visualization. This has been fixed now.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.

3.7.0

Nextclade 3.7.0

Use Auspice JSON as a full dataset (experimental)

Nextclade can now optionally use Auspice datasets (in Auspice v2 JSON format) not only as reference trees, but also as self-contained full Nextclade datasets. Nextclade will take pathogen info, genome annotation, reference sequence, and, of course, reference tree from Auspice JSON. No other files are needed. This allows to use almost any Auspice dataset (e.g. from nextstrain.org) as Nextclade dataset.

• In Nextclade CLI, --input-dataset argument now also accepts a path to Auspice JSON file (in addition to accepting the usual paths to a dataset directory and zip archive)

• Nextclade Web now has a new URL parameter dataset-json-url, which accepts a URL to Auspice JSON file or even to a dataset URL on nextstrain.org

This feature is currently in experimental stage. For details and discussion see PR #1455.

Make reference tree branch attributes optional

Nextclade now accepts Auspice JSONs without .branch_attrs on tree nodes.

Allow index and seqName in column selection

Previously, Nextclade treated output CSV/TSV columns index and seqName as mandatory and they were always present in the output files. In this release they are made configurable. One can:

• in CLI: add or omit index and seqName values when using --output-columns-selection argument
• in Web: tick or untick checkboxes for index and seqName in "Column config" tab of "Export" page

Add dataset capabilities

The table in the nextclade dataset list command now displays an additional column "capabilities", which lists dataset capabilities, i.e. whether dataset contains information allowing clade assignment, QC, etc. The same information is available in JSON format (unstable) if you pass --json flag.

Installation and usage 📚 Documentation: docs.nextstrain.org/projects/nextclade 🌍 Nextclade Web: clades.nextstrain.org 🖥️ Nextclade CLI: 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. 🐋 Docker images are available on DockerHub 🐍 Conda package is available in bioconda channel.