Primer Prospector is a pipeline of programs to design and analyze PCR primers.

De novo primers can be generated from a set of aligned fasta sequences and these primers, or known primers from the literature, can be scored against target sequences. Predicted primer performance can be visualized in summary graphs showing overall primer performance or across specific taxonomies. Primer Prospector is built in Python using the open-sourcePyCogent toolkit. William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, and Rob Knight. Bioinformatics, 2011; doi:10.1093/bioinformatics/btr087