PolyOligo

Design oligos for complex genomes. (alpha version)

What Is It?

A Python-based multicore enabled set of tools to design oligonucleotides. Supports SNPs and indels and can use known mutations across populations to refine designs.

A webapp version of this software is available HERE !

Included binaries (click on the command for more information)

• polyoligo-pcr: Standard PCR or Sanger sequencing primers.
• polyoligo-kasp: Genotyping by Kompetitive allele specific PCR (KASP).
• polyoligo-caps: Genotyping by Cleaved Amplified Polymorphic Sequences (CAPS).
• polyoligo-hrm: Genotyping by high-resolution melting (HRM) PCR.
• polyoligo-crispr: Guide RNAs for CRISPR/Cas9 assays.

Getting Started

The software has a command-line interface which is accessed using your favorite terminal. Note that all positions use a 1-based indexing.

Prerequisites

OS: MacOSX or Linux

Python v3 or newer

To check if Python3 is installed on your system run the following command:

python3 -V

If the command failed install Python3 for your OS from the official Python website.

It is also recommended to use the lastest version of pip and setuptools, which can be installed by running the command:

python3 -m pip install -U pip setuptools --user

Installation

Installation is done directly from source. For that, clone this repository using the commands:

git clone https://github.com/MirkoLedda/polyoligo.git
cd polyoligo

If you do have sudo permissions, such as on a personal laptop, then use the command:

sudo python3 setup.py install

Otherwise, run a local installation using the commands:

python3 setup.py install --user
echo 'export PATH="$PATH:~/.local/bin"' >> ~/.bashrc; source ~/.bashrc

Running a test

To make sure the installation ran properly, run:

polyoligo

Citation

Ledda M., Cobo N., Lorant A., Hardigan M.A. and Knapp S.J., PolyOligo: A Bioinformatic Platform for Identifying Target DNA Sequences for the Development of Sub-Genome Specific DNA Markers in Polyploid/Complex Genomes. Poster presented at: Annual Conference of the American Society of Horticultural Sciences; 2019 July 21-25; Las Vegas, NV, USA

Reporting bugs and requesting features

This software is actively supported and all changes are listed in the CHANGELOG. To report a bug open a ticket in the issues tracker. Features can be requested by opening a ticket in the pull request.

Contributors

• Mirko Ledda - Initial implementation and developer
• Nicolas Cobo - Requirements and biological accuracy

License

This software is licensed under the BSD-2 License - see the LICENSE file for details.