Skip to main content

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

Project description

# Selective whole genome amplification
[![Build Status](https://travis-ci.org/eclarke/swga.svg?branch=master)](https://travis-ci.org/eclarke/swga)
[![Coverage Status](https://coveralls.io/repos/eclarke/swga/badge.svg?branch=dev&service=github)](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.

Project details


Release history Release notifications

This version
History Node

0.4.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
swga-0.4.0-py2-none-any.whl (189.9 kB) Copy SHA256 hash SHA256 Wheel py2 Nov 20, 2015
swga-0.4.0.tar.gz (28.7 kB) Copy SHA256 hash SHA256 Source None Nov 20, 2015

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page