---

title: 'pcr-marker-design' ...

Tools for PCR assay design from NGS variant data

Galaxy-free refactoring of https://github.com/cfljam/galaxy-pcr-markers

Usage

Installation

• create and activate a clean Python 3xx env

e.g.

conda create -y -n Py3PCRtest python=3.5  numpy cython bedtools
source activate  Py3PCRtest

• optionally append jupyter notebook (or just ipykernel ) for usage in notebooks

conda install  jupyter notebook

• pull this repo

git clone https://github.com/PlantandFoodResearch/pcr_marker_design

• pip install it

pip install ./pcr_marker_design

For development work

pip install -e ./pcr_marker_design

Create an identical env

• in OSX

conda create --name <env> --file ./docs/Py3_environment.spec.txt

• other (may need some editing)

conda env create -f ./docs/Py3_environment.yml

Requirements

Python 3.5

To Run Tests

from root directory

pytest

Melt Prediction

• Relies on Univ of Utah Wittwer Lab Service
• See a test by visting https://www.dna.utah.edu/db/services/cgi-bin/udesign.cgi?seq=CTGATCGATCGTACGGCGCATCGTAGCTCWTAGCTACGCGCGTAGCTAGCTGCCGTAGC&rs=0&cation=20&mg=2&dmso=0

Compatibility

Licence

Authors

pcr-marker-design was written by John McCallum , Susan Thomson Leshi Chen, Scout Liu Brett DavisTim Millar