ARTIC pipeline

In this part of the tutorial we are going to use the ARTIC pipeline to generate consensus sequences from our ARTIC amplicon data. We will then polish the consensus with Illumina data using Pilon. As a final step, we will run Nextstrain with example SARS-Cov2 data and include our own sequences.

• ARTIC pipeline
• Polishing with pilon
• Get the remaining results
• Nextstrain