Minimal Residual Disease (MRD) monitoring is crucial in ALL treatment as it strongly predicts patient outcomes and guides therapeutic decision-making. NGS has become increasingly important for MRD detection in ALL. While NGS provides comprehensive marker identification, it has limitations in amplification bias and quantification accuracy. Unique Molecular Identifiers (UMIs) help overcome these challenges by enabling precise counting, reducing bias, and improving error correction, potentially enhancing MRD quantification accuracy. Currently, there is no end-to-end so ware solution for processing UMI-based T/B-Cell Receptor sequencing data for MRD assessment. QuaSIR is an operator independent nomenclature agnositc framework that processes FASTQs derived from sequencing of UMI-tagged multiplexed PCR of DNA extracted from bone marrow samples. Depending on the timepoint of the sample, QuaSIR then identifies clones that are markers for leukemic blasts, or tracks marker clones in follow up samples. QuaSIR then generates a user-friendly medical report to aid the clinician in therapeutic interventions.