A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design.
primer design dna sequencing next-generation sequencing amplicon sequencing pcr primer dimer bio-barcodes multiplex