swga 0.4.0

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

# Selective whole genome amplification
[](https://travis-ci.org/eclarke/swga)
[](https://coveralls.io/github/eclarke/swga)
## 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](https://github.com/eclarke/swga/wiki/Installation)

## Using SWGA
Follow the guide on our Wiki/[Quick Start](https://github.com/eclarke/swga/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](https://github.com/eclarke/swga/wiki/Installation).

## 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.