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.
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.
- Current test coverage (
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.
This new version of
find_differential_primers) now uses a subcommand model, like the tools
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.
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.
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