Output files

This section describes the files produced by Nextclade Web and Nextclade CLI run subcommand.

You can download these files from Nextclade Web, after completing an analysis run, using the “Export” dialog.

You can request one or multiple output files from Nextclade CLI by providing paths into a family of output arguments to the run subcommand (they start with --output-).

• All outputs
• Nucleotide alignment
• Translations
• Analysis results (tabular)
• Analysis results (JSON)
• Phylogenetic tree
• Errors and warnings
• Compression, stdout