Nextclade: analysis of viral genetic sequencesď
Note
If you are migrating from Nextclade v2 to Nextclade v3, please read our Nextclade v3 migration guide
Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.
Nextclade consists of a set of related tools:
Nextclade Web - a web application available online at clades.nextstrain.org
Nextclade CLI - a command-line tool
Both tools are powered by the same algorithms, they consume the same inputs and produce the same outputs, but they differ in the user interface, the features included, and the degree of customization. It is recommended to start with Nextclade Web and later proceed to CLI tools if you have more advanced use-cases (for example, repeated batch processing, bioinformatics pipelines).
Nextclade is a part of Nextstrain, an open-source project to harness the scientific and public health potential of pathogen genome data. All source code is available on GitHub.
Note
Referring to Nextclade in a publication
If you use results obtained with Nextclade in a publication, please
cite our paper:
Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773
where possible, provide a link to Nextclade Web:
Note
Do you find Nextclade useful? Tell us about your use-case and experience with it.
For a general conversation, feel free to join Nextstrain Discussion at discussion.nextstrain.org.
If you want to report an error or request a new feature, please open a new Github Issue (despite the name, âGithub Issuesâ can be about anything, not only problems).
Table of contents
- Home
- Migration to Nextclade v3
- 1. Nextalign CLI is removed
- 2. Some alignment parameters are removed
- 3. Different tree output
- 4. Dataset file format and dataset names have changed
- 5. Some CLI arguments for individual input files are removed
- 6. Some output files are removed
- 7. Genome annotation CLI argument is renamed
- 8. URL parameters in Nextclade Web have changed
- Nextclade Web
- Nextclade CLI
- Nextclade datasets
- Input files
- Output files
- Algorithm
- Useful links
- Frequently asked questions
- Terminology
- Reference sequence
- Root sequence
- Query sequence
- Reference nucleotide
- Query nucleotide
- Gene
- Codon (concept)
- Codon (position)
- Peptide
- Query peptide
- Reference peptide
- Query aminoacid
- Reference aminoacid
- Reference tree (concept)
- Reference tree (file)
- Reference node
- Root node
- New node
- Gene map
- Alignment (process)
- Alignment (result)
- Alignment range
- Clade
- Phylogenetic placement
- Analysis
- Branch length
- Divergence
- Frame
- Frame shift
- Recent changes