Scripts to aid the design of differential primers for diagnostic PCR.
Python
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diagnostic_primers
git_hooks
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.codecov.yml
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CITATION
LICENSE
README.md
pdp.py
requirements.txt
setup.py

README.md

README.md (diagnostic_primers)

NOTE FOR USERS

The default branch for this repository is a development branch: diagnostic_primers. If you are looking for code to reproduce work in Pritchard et al. (2012) or Pritchard et al. (2013), please checkout the master branch, or download release v0.1.3.

  • diagnostic_primers:

codecov Build Status

  • master:

codecov Build Status

NOTE FOR DEVELOPERS

The default master branch for development is diagnostic_primers. We would appreciate contributions, especially if you follow the guidelines on the wiki.

Overview

This repository contains code for automated finding of discriminatory (real-time) PCR or qPCR primers that distinguish among genomes or other biological sequences of interest.

Usage

This new version of diagnostic_primers (formerly find_differential_primers) now uses a subcommand model, like the tools git and subversion. These execute the following subtasks, some or all of which may be required in a primer design run.

  • process: Validate the configuration file and stitch input contig fragments/replace ambiguity symbols as necessary.
  • prodigal: Predict CDS locations on the input sequence
  • eprimer3: Design amplifying primers on the input sequence
  • blastcheck: Filter designed primers against a database of negative examples
  • primersearch: Filter designed primers on their ability to amplify each input sequence
  • classify: Classify designed primers by specificity for each class of input sequence

Each of these subcommands has specific help, accessible with pdp.py <subcommand> -h or pdp.py <subcommand> --help.

FURTHER INFORMATION:

Please read the comments contained within the top of each '*.py' file as well as the Supporting Information ('Methods S1' document) of doi:10.1371/journal.pone.0034498.

CONTRIBUTORS

CITATIONS

Please refer to the following for methodological details:

  • Pritchard L et al. (2012) "Alignment-Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains." PLoS ONE 7(4): e34498. doi:10.1371/journal.pone.0034498 - Method description and application to human bacterial pathogens, sub-serotype resolution
  • Pritchard L et al. (2013) "Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences." Plant Pathology, 62, 587-596 doi:10.1111/j.1365-3059.2012.02678.x - Application to plant pathogens, species-level resolution