Design PCR primers from DNA sequence. Widely used (190k Google hits for “primer3”). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl.

Installing

sudo apt-get install -y build-essential g++ cmake git-all

git clone https://github.com/primer3-org/primer3.git primer3

cd primer3/src

make

make test

Run Primer3

./primer3_core ../example

Read the complete Primer3 manual

Primer3 Manual

or see /src/primer3_manual.htm