PriSM

The program PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity. PriSM uses alignments of previously sequenced viral genomes to select, filter, and match amplification primers that can be used to maximize the captured diversity of the viral population within future samples. The primer and amplicon selection criteria can be customized depending on the needs of the user. PriSM is the first program we are aware of that facilitates primer design to capture the full viral genome while maintaining population diversity through the use of degeneracy in the design phase.

Access PriSM here.