OligoN-Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets

Area of Science:

• Ecology
• Evolutionary Biology
• Bioinformatics

Background:

• High-throughput environmental DNA sequencing generates vast datasets, creating a bottleneck in designing specific oligonucleotides for molecular studies.
• Existing tools struggle with large datasets and often rely on predefined databases or complex analyses, limiting their applicability.

Purpose of the Study:

• To present oligoN-design, a versatile software tool for designing taxon-specific oligonucleotides from custom sequence sets.
• To provide a solution that is simple, reproducible, and adaptable to high-throughput sequencing data analyses.

Main Methods:

• oligoN-design requires two FASTA files: one for target taxa and one for non-target taxa.
• The tool integrates with standard bioinformatics software like BLAST, VSEARCH, and MAFFT.
• It offers both unsupervised end-to-end usage and detailed expert usage options.

Main Results:

• oligoN-design successfully replicates known taxa-specific oligonucleotides using large ribosomal databases (PR2, SILVA).
• The process is efficient, completing in under 30 minutes with minimal RAM (6 GB) on a personal laptop.
• The software is adaptable for various strategies, from automated to expert-driven design.

Conclusions:

• oligoN-design overcomes the oligonucleotide design bottleneck in big data molecular ecology and evolutionary studies.
• Its simplicity, efficiency, and adaptability make it a valuable tool for researchers working with large environmental DNA datasets.
• The software is freely available and easily installable via bioconda.