Templated long-read workflow (ARTIC)

As described in the ARTIC Amplicon workflow topic, many researchers working with viral genomes will start with draft genomes, while some will start with raw (unassembled) Nanopore or PacBio long-read data that requires assembly. This tutorial is in two parts, one for each type of researcher. Therefore, unlike most of our Lasergene tutorials, each part of the tutorial is self-contained. You can do either of them without doing the other.

• Part A of this tutorial represents the starting point for those researchers who have only raw long-read data in PacBio CLR, PacBio HiFi or Nanopore format. In this part, you will create draft genome assemblies for seven SARS-CoV-2 samples using SeqMan NGen. You will then open one of the assemblies in SeqMan Ultra, generate a table of non-synonymous variants, and export one of the consensus sequences (i.e., “draft genomes”) in .fasta format. You can either stop at this point or proceed to Part B for further analysis of the experimental sample. If you only work with draft genomes rather than raw long reads, you may skip Part A and proceed directly to Part B.

• Part B of this tutorial is the starting point for researchers who already have draft genomes in any format and an optional method of analysis for researchers who began with raw long-read data and followed the steps in Part A. In Part B, you will use MegAlign Pro to compare an experimental SARS-CoV-2 sample to reference sequences from four SARS-CoV-2 variants to determine which variant that the sample has.