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MatthewHiggins2017 / bioconda-PrimedRPA

GNU General Public License v3.0
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PrimedRPA

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A python-based command-line package to augment primer and probe design for Recombinase Polymerase Amplification (RPA).

Installation

GitHub Installation

git clone https://github.com/MatthewHiggins2017/bioconda-PrimedRPA.git
cd ./bioconda-PrimedRPA
conda env create --file=PrimedRPA.yml
conda activate RPA
python setup.py install

Conda Installation

conda install -c bioconda primedrpa

Parameter Parsing

Parameters can be parsed to PrimedRPA via the command line or using the PrimedRPA_Parameters.txt file. To download the text file please see the link below:

wget https://raw.githubusercontent.com/MatthewHiggins2017/bioconda-PrimedRPA/master/PrimedRPA_Parameters.txt

Key Output Files

For each PrimedRPA run the following 3 key files are generated:

[RunID]_Alignment_Summary.csv
[RunID]_Oligo_Binding_Sites.csv
[RunID]_Output_Sets.csv

Walk-Through

Please see the wiki for more information, including a step-by-step walk through of using the software.

3rd-Party Software

PrimerRPA incorporates the following 3rd party software:

Clustal Omega (http://www.clustal.org/omega/) - For sequence alignment if necessary.
Blastn (https://blast.ncbi.nlm.nih.gov/Blast.cgi) - To assess primer/probe cross-reactivity.
Samtools (http://www.htslib.org/) - To assess primer/probe cross-reactivity.

Contact

If you encounter any bugs please contact me directly at matthew.higgins[at]lshtm.ac.uk