variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.
For a lot of virus genera it is difficult to design pan-specific primers. varVAMP solves this by introducing ambiguous characters into primers and minimizes mismatches at the 3' end. Primers might not work for some sequences of your input alignment but should recognize the large majority.
varVAMP comes in three different flavors:
SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.
TILED: varVAMP uses a graph based approach to design overlapping amplicons that tile the entire viral genome. This designs amplicons that are suitable for Oxford Nanopore or Illumina based full-genome sequencing.
QPCR: varVAMP searches for small amplicons with an optimized internal probe (TaqMan). It minimizes temperature differences between the primers and checks for amplicon secondary structures.
We, in collaboration with specialists for the respective viruses, have already designed and wet-lab evaluated primer schemes for various viral pathogens. All the input data and varVAMP outputs are freely available here.
Moreover, varVAMP primers are now available at primerschemes. varVAMP now reports primer bed files in ARTICv3 format. Feel free to contribute newly designed schemes via this Github repository of the QuickLab. Use primal-page developed by Chris Kent to generate data for compatible pull-requests.
varVAMP: automated pan-specific primer design for tiled full genome sequencing and qPCR of highly diverse viral pathogens.
Important disclaimer: For the primer design, varVAMP uses primer3 to check if digested kmers of a sequence are potential primers. Some of the functions for this were adapted from primalscheme and I do not claim credit.
The remaing code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.