umite: fast quantification of Smart-seq3 libraries with improved UMI retrieval

ABSTRACT Commercial solutions like 10X cellranger provide robust UMI quantification for their proprietary single-cell protocols, but open methods such as Smart-seq3 lack comparable support. Here, we introduce umite, a Smart-seq3 UMI counting pipeline with a focus on speed and a light memory footprint. Unlike existing tools, umite offers efficient mismatch-tolerant UMI detection, boosting UMI retrieval by 5-15% in benchmarks. It also outperforms current Smart-seq3 quantification tools in runtime, disk usage, and memory footprint, offering better scalability on large datasets. Availability and Implementation: umite is available at https://github.com/leoforster/umite and includes a Snakemake workflow for Smart-seq3 quantification. Single cell libraries of the mouse nasal vasculature dataset (GSE207085) and human CD4+ T-cell dataset (GSE270928) used in benchmarking were downloaded from NCBI (see Supplement for details).