Nextclade CLI

Nextclade CLI is a command-line tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data. You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.

💡 Nextclade CLI is suitable for advanced users requiring large-scale analysis and integration into bioinformatics pipelines. For a simpler, more user-friendly tool, try Nextclade Web.

This section describes:

  • how to install Nextclade CLI - using Docker, as a standalone executable, or using conda

  • how to run Nextclade CLI with sample data

  • what other sections of the documentation are worth checking after that