PyPI version and Licensing¶
pdp is a program and Python package (
diagnostic_primers) that provides support for design and identification of diagnostic qPCR and metabarcoding primers and marker sequences. It performs automated finding of discriminatory (real-time) PCR or qPCR primers that distinguish among genomes or other biological sequences of interest. It is also useful for the identification of metabarcoding marker sequences that can discriminate within a subset of bacterial genomes.
pdp natively takes advantage of multicore systems, and can integrate with SGE or OGE-compatible job schedulers to manage the computationally-heavy sequence comparisons.
This package can be used with either of two command-line interfaces:
find_differential_primers.py, which maintains backwards compatibility with the old
find_differential_primers package, and
pdp, which is a new step-wise interface for scripting and performing specific stages of the design in isolation. The ability to separate out individual stages allows for scripting of branching designs, where alternative design filters and parameters may be used.
find_differential_primers.py interface may be deprecated in a future release.
Reporting problems and requesting improvements¶
If you encounter bugs or errors, or would like to suggest ways in which
pdp can be improved, please raise a new issue at the
pdp GitHub issues page.
If you’d like to fix a bug or make an improvement yourself, contributions are welcomed, and guidelines on how to do this can be found at the Contributing to pdp documentation page.
- QuickStart Guide
- Installation Guide
- Contributing to