swga

Pipeline to select compatible primer sets for selective whole-genome amplification.


License
Other
Install
pip install swga==0.4.0

Documentation

Selective whole genome amplification

Build Status Coverage Status

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 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.