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bioRxiv · 10.1101/2025.07.15.664946

Detecting Foldback Artifacts in Long Reads

Heinz, J. M.·Meyerson, M.·Li, H.
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Abstract

Long-read sequencing data is useful for detecting large and complex structural variations; however, technical artifacts can lead to false structural variant calls. In our analyses, we became aware of a foldback artifact in long-read data. Therefore, we developed the open-source Breakinator tool to flag putative foldback artifact reads, as well as previously known chimeric artifacts. Through an alignment-based approach, Breakinator can detect artifacts missed by existing quality control tools. We profiled the occurrences of foldbacks and chimeric reads in both Oxford Nanopore and PacBio sequences across a range of specimens, library types, sequencing chemistries, sequencing machines, and base-calling software.

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Heinz, J. M., Meyerson, M., Li, H.. 2025-07-18. Detecting Foldback Artifacts in Long Reads. https://doi.org/10.1101/2025.07.15.664946

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