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bioRxiv · 10.1101/2025.07.15.664951

Quality control of single-cell ATAC-seq data without peak calling using Chromap

Ahmed, O.·Zhang, H.·Langmead, B.·Song, L.
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Abstract

In this work, we extend Chromap, an ultrafast method for single-cell ATAC-seq data alignment, to directly report peak-based quality control (QC) metrics, such as the fraction of reads in peaks, without calling peaks. Recent single-cell ATAC-seq analysis methods like SnapATAC2 utilize the genome-interval-based feature for data analysis, which disables filtering low-quality cells using common peak-based QC metrics. We show that Chromaps QC metrics capture additional low-quality cells missed by SnapATAC2 and improve downstream analysis results without sacrificing computational efficiency.

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Ahmed, O., Zhang, H., Langmead, B., Song, L.. 2025-07-18. Quality control of single-cell ATAC-seq data without peak calling using Chromap. https://doi.org/10.1101/2025.07.15.664951

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