Figure 1.

The periscope ARTIC Nanopore algorithm design details. (A) ARTIC network amplicon layout with respect to ORF TRS positions of SARS-CoV-2. Blue and aqua at the end of each ORF signifies leader and TRS, respectively. (B) Read pileup at ORF6 TRS showing two types of reads that support the existence of sgRNAs. Type 1 (red) is results from 3′→5′ amplification from the closest primer to the 3′ of the TRS site, and type 2 (green) is results from 3′→5′ amplification from the adjacent amplicons 3′ primer (i.e., the second closest 3′ primer). (C) Overview of the periscope workflow. (D) Decision tree for read classification. Green arrow denotes a “yes” for the step-in question; namely, if the read is at a known ORF start site, a green arrow is used; if not, a red arrow for “no” is used.