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Algorithm
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Internally, Nextclade is implemented as a parallel pipeline which consists of several steps. This section describes these steps, roughly in their order of execution.

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

    01-sequence-alignment.md
    02-translation.md
    03-phylogenetic-placement.md
    04-clade-assignment.md
    05-mutation-calling.md
    06-quality-control.md
    07-pcr-primer-changes-detection.md
    nextclade-pango.md