UMIche: A UMI-centric analysis platform for enhancing molecular quantification accuracy in bulk and single-cell sequencing

Unique molecular identifiers (UMIs) are widely utilised in RNA sequencing (RNA-seq) technologies to eliminate polymerase chain reaction (PCR) duplicates, thereby improving the accuracy of molecular quantification. However, synthesis errors in UMIs during sequencing often compromise the reliability of UMI counting. While various computational methods have been developed for error correction, the lack of a unified benchmarking and validation framework impedes systematic evaluation and optimisation. Here, we present UMIche, an open-source, UMI-centric computational platform designed to enhance UMI-assisted molecular quantification by offering a systematic, integrative, and extensible framework for UMI analysis. We show that through its integration of a broad spectrum of UMI collapsing methods and workflows, UMIche significantly advances the accuracy of molecular quantification and facilitates the generation of high-fidelity gene expression profiles.