MitoChontrol: Adaptive mitochondrial filtering for robust single-cell RNA sequencing quality control

Abstract

SummaryMitochondrial transcript abundance is a standard quality control metric in single-cell RNA sequencing, but fixed percentage thresholds fail to account for the substantial variation in mitochondrial content across cell types and tissues, risking both retention of compromised cells and exclusion of transcriptionally active viable cell populations. We present MitoChontrol, a cell-type-aware probabilistic framework for mitochondrial quality control that models the mitochondrial transcript fraction within transcriptionally coherent clusters as a Gaussian mixture distribution. Compromised-cell components are identified from the upper tail of each cluster-specific distribution, and filtering thresholds are defined as the point at which the posterior probability of cellular compromise exceeds a user-definded confidence value. Applied to controlled perturbation experiments and a pancreatic ductal adenocarcinoma single-cell dataset, MitoChontrol selectively removes transcriptionally compromised cells while preserving biologically elevated but viable populations, outperforming fixed-threshold and outlier-based approaches. Availability and ImplementationMitoChontrol is implemented in Python and integrates directly with AnnData-based workflows. It is freely available under the GNU General Public License v3 (GPL-3.0) at: https://github.com/uttamLab/MitoChontrol (DOI: https://doi.org/10.5281/zenodo.19423054)