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ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

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Detecting foldback artifacts in long-reads.

Jakob M Heinz^1,2,3, Matthew Meyerson^3,4,5, Heng Li^6,7

¹Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

|January 6, 2026

Summary

This summary is machine-generated.

A new tool, Breakinator, identifies foldback artifacts in long-read sequencing data, improving structural variant detection accuracy. This open-source software flags potential errors missed by other quality control methods.

Keywords:

Long-read sequencing Nanopore Quality control RNA-Sequencing Technical artifacts

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Long-read sequencing is valuable for identifying complex structural variations.
Technical artifacts in sequencing data can lead to inaccurate structural variant calls.
A specific foldback artifact in long-read data was identified.

Purpose of the Study:

To develop an open-source tool, Breakinator, for detecting foldback artifacts in long-read sequencing data.
To identify and flag reads containing foldback and chimeric artifacts.
To assess the prevalence of these artifacts across various sequencing platforms and conditions.

Main Methods:

Developed Breakinator, an open-source bioinformatics tool.
Utilized an alignment-based approach for artifact detection.
Analyzed Oxford Nanopore and PacBio sequencing data.

Main Results:

Breakinator successfully flags putative foldback artifact reads.
The tool detects artifacts that may be missed by existing quality control methods.
Foldback and chimeric read occurrences were profiled across diverse sequencing parameters.

Conclusions:

Breakinator enhances the accuracy of structural variant detection from long-read sequencing data.
The tool provides a valuable quality control measure for genomic analyses.
Understanding and mitigating sequencing artifacts is crucial for reliable genomic variation discovery.