This is an easy-to-use, start-to-end package for finding sets of primers that selectively amplify a particular genome (the "foreground" genome) over a background genome. For instance, we can design a set of primers that amplify a parasite's genome in a sample that is overwhelmingly composed of host DNA.

You can run SWGA on hardware ranging from a Mac laptop to a high-end server.

• Counts all the possible primers in a size range in both genomes
• Filters primers based on:
  • foreground and background genome binding rates
  • melting temperatures (with a built-in melt temp calculator that accounts for mono- and divalent cation solutions!)
  • Possible homodimerization
• Finds primer sets containing primers that are compatible with each other using graph theory (largest clique formation). The process ensures:
  • No primer in a set is a heterodimer
  • Even binding site spacing in foreground genome
  • Low total binding to background genome
• Score each set based on certain binding metrics and allows exploration of high-scoring sets via output to common formats.

Follow the installation instructions here

Follow the guide on our Wiki/Quick Start to get started!

New features and bugfixes are released all the time. To update, simply follow steps 3-5 on the installation instructions.