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Input files
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This section describes input files for Nextclade Web and Nextclade CLI `run` subcommand, their expected formats as well as how they are used in Nextclade Web and Nextclade CLI.

..  toctree::
    :titlesonly:
    :maxdepth: 2

    01-sequence-data.md
    02-reference-sequence.md
    03-genome-annotation.md
    04-reference-tree.md
    05-pathogen-config.md
    compression