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Overview

UniAmp (Unique Amplicon) is a computational pipeline to generate PCR primers specific to a target genome.

The UniAmp pipeline can be conceptually split into 4 parts:

1. Build directory of query genomes with high sequence similarity to target genome.
2. Retrieve unique sequences in a target genome compared to query genomes.
3. Select unique target sequence for primer design.
4. Design primers to unique target sequence.

Visual representation:

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Installation

Clone the repository:

git clone https://github.com/kenscripts/UniAmp.git

Run the setup script and specify UniAmp path:

source <path_to_UniAmp>/UniAmp/setup_uniamp.sh <path_to_UniAmp>

Documentation

Further information, including how to use UniAmp, is available at: https://uniamp.readthedocs.io/en/latest/

Citation

If you use UniAmp in your research, please cite:

Acosta, K., Sorrels, S., Chrisler, W., Huang, W., Gilbert, S., Brinkman, T., Michael, T. P., Lebeis, S. L., & Lam, E. (2023). Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria. Plants, 12(4), 872. https://doi.org/10.3390/plants12040872