MPD: multiplex primer design for next-generation targeted sequencing
Wingo, T.S., Kotlar, A., Cutler, D.J.
Targeted resequencing offers a cost-effective alternative to whole-genome and whole-exome sequencing when investigating regions known to be associated with a trait or disease. There are a number of approaches to targeted resequencing, including microfluidic PCR amplification, which may be enhanced by multiplex PCR. Currently, there is no open-source software that can design next-generation multiplex PCR experiments that ensures primers are unique at a genome-level and efficiently pools compatible primers.
MPD can successfully design multiplex PCR experiments suitable for next-generation sequencing, and simplifies retooling targeted resequencing pipelines to focus on new targets as new genetic evidence emerges.
Wingo, T.S., Kotlar, A., Cutler, D.J. "MPD: multiplex primer design for next-generation targeted sequencing" BMC Bioinformatics (2017): 14