Fig. 4: Head-to-head benchmark of the variant awareness of varVAMP, Olivar and PrimalScheme.
From: varVAMP: degenerate primer design for tiled full genome sequencing and qPCR
a Cumulative counts of mismatches between primers and sequences in the MSA. For each primer the number of mismatches with each sequence of the MSA was counted if it was not covered by any primer permutation. Shown are the cumulative mismatches between primers and MSA sequences in the tiled primer schemes for the respective viruses. The dot area size is proportional to the percentage. b Analogous to a the mismatches with the MSA sequences were counted per primer nucleotide position and averaged over all primers in a scheme. As primers vary in their length, the % mismatches are displayed starting at the primer’s 3’ end (position 0 is the most 3’ nucleotide position). The gray triangle schematically indicates the primer positions that varVAMP penalizes and the position-specific penalty multipliers (32, 16, 8, 4, 2).
