I have finished analysing my data from an Illumina MiSeq run of intestinal bacteria. Since this data only provides relative rather than absolute abundances of bacteria, I would like to run some qPCR analyses to quantify some of the more abundant families, for example Bacteroidaceae, Lachnospiraceae, etc.

Is there a program available that will allow me to design taxa specific primers from my own sequences or would I be best just going with previously published sequences specific for Lachnospiraceae?

Many thanks!