oligoN-design

The purpose of this tool is to help the user design specific oligonucleotide, to be later used as probes for Fluorescence in situ Hybridisation (FISH) or primers for PCR amplification. It focuses on Small SubUnit (SSU) of the rDNA operon (18S rDNA and 16S rDNA), but can potentially be used for other genes.

For a detailed documentation of the OligoN-design tool, please see the documentation.

brief_pipeline

Installation

OligoN-design is available from bioconda, and the simplest option to install oligoN-design is to use micromamba (or conda or mamba). So before starting, please make sure you have micromamba installed.
Once micromamba is installed, open the bash terminal, go to your preferred environment and run:

micromamba install oligon-design

Otherwise, you can create a new environment as follows:

micromamba create --name oligoNenv oligon-design

Then simply activate the environment to run oligoN-design functions (micromamba activate oligoNenv ), and deactivate it to exit (‘micromamba deactivate’).
Please, note that you can replace oligoNenv by the environment name of your choice.

For further information about installation, see the bioconda webapge.

Running

After activating the oligoN-design environment, you can start running the functions as follow:

sequenceSelect -f database.fasta -p pattern -o target.fasta
sequenceSelect -f database.fasta -p pattern -o excluding.fasta -r
oligoNdesign -t target.fasta -e excluding.fasta -o oligos

You can find other examples, suggested workflows and even “common problems and misconceptions” or “good practices” in the documentation.

Citing

If you use the oligoN-design tool to either design specific oligonucleotides, or to help you design specific oligonucleotides, please cite the following manuscript where we report this software:

Sandin MM, Walde M, Henry N, Berney C, Simon N, Forn I, Massana R, Richter D (2025) OligoN-design: A simple and versatile tool to design specific probes and primers from large heterogeneous datasets. Mol. Ecol. Resour. 26(3): e70140. doi: 10.1111/1755-0998.70140

Concluding remarks

The OligoN-design tool was designed to help the design of specific oligonucleotides accommodating the large environmental datasets and with a simple and versatile approach. However, any output from this tool should be interpreted as a starting point and needs to be empirically optimized and tested.