minnow

Minnow is a comprehensive simulation framework for droplet-based single-cell RNA-sequencing (dscRNA-seq) experiments that generates realistic sequence-level data. It models various aspects of the experimental process, such as PCR amplification, cellular barcodes, unique molecular identifiers (UMIs), sequence fragmentation, and sequencing. Minnow also incorporates gene-level ambiguity characteristics observed in real scRNA-seq datasets. The tool allows researchers to assess the performance of different processing pipelines that generate gene-by-cell count matrices from raw dscRNA-seq data. By simulating realistic datasets, minnow helps evaluate the impact of factors such as read alignment and UMI deduplication methods on accurate quantification, which are often overlooked when using simulated count matrices.