Selective whole genome amplification

Introduction

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.

Features:

• 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.

Installation

Follow the installation instructions here

Using SWGA

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

Updates

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

3rd-party code

SWGA incorporates code from other open-source projects:

• cliquer, a clique-finding library by Sampo Niskanen and Patric Ostergard
  • http://users.aalto.fi/~pat/cliquer.html
• DSK, a disk-based kmer-counting tool by G. Rizk
  • http://minia.genouest.org/dsk/
  • Citation: (Rizk, G., Lavenier, D. and Chikhi, R. DSK: k-mer counting with very low memory usage, Bioinformatics, 2013.)

Cliquer is copyright © 2002 Sampo Niskanen, Patric Östergård. and licensed under the GPL.

DSK is licensed under the CeCILL license, which can be found in src/dsk/LICENSE, and is GPL compatible.