Algorithm

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

• 1. Sequence alignment
• 2. Translation
• 3. Phylogenetic placement
• 4. Clade assignment
• 5. Mutation calling
• 6. Quality Control (QC)
• 7. Detection of PCR primer changes
• Nextclade as pango lineage classifier: Methods and Validation