Oligo Designer Toolsuite

Oligonucleotides (abbrev. oligos) are short, synthetic strands of DNA or RNA that are designed with respect to a specific target region and have many application areas, ranging from research to disease diagnosis or therapeutics. Oligos can be used as primers during DNA amplification, as probes for in situ hybridization or as guide RNAs for CRISPR-based gene editing. Based on the intended application and experimental design, researchers have to customize the length, sequence composition, and thermodynamic properties of the designed oligos.

Various tools exist that provide custom design of oligo sequences depending on the area of application. Even though most tools apply the same basic processing steps, ranging from the generation of custom-length oligo sequences, the filtering of oligo sequences based on thermodynamic properties as well as the selection of an optimal set of oligos, each newly developed tool uses its own implementation and different package dependencies. Consequently, not only the development of new tools is slowed down, but also the maintenance and modification of existing tools is hampered, because developers do not have a common resource for those functionalities to use. We tackle this issue with our open-source Oligo Designer Toolsuite.

Oligo Designer Toolsuite is a collection of modules that provides all basic functionalities for custom oligo design pipelines as well as advanced experiment-specific functionalities like machine learning models for oligo specificity prediction within a flexible Python framework.

To allow the flexible usage of different modules, depending on the required processing steps, we developed a common underlying data structure that ensures the cross-compatibility of all modules within the framework. This data structure is runtime and memory optimized to enable the processing of large sequence dataset in a reasonable time frame. With our Oligo Designer Toolsuite we aim to set new standards in the development of oligo design pipelines, helping to accelerate the development of new tools and facilitate the upgrade of existing tools with the latest developments in the field. We also provide ready-to-use oligo design pipelines for specific experimental setups, e.g. MERFISH or SeqFISH+ probe design for Spatial Transcriptomics.