# Detecting foldback artifacts in long-reads

## TL;DR

This paper introduces Breakinator, a tool to detect foldback and chimeric artifacts in long-read sequencing data, improving the accuracy of structural variant calls.

## Contribution

The novel contribution is the development of Breakinator, an open-source tool that detects foldback artifacts missed by existing quality control methods.

## Key findings

- Breakinator successfully identifies foldback and chimeric artifacts in long-read data.
- Foldback artifacts were found to occur across various sequencing platforms and conditions.
- The tool improves the reliability of structural variant detection in long-read sequencing.

## 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.

The online version contains supplementary material available at 10.1186/s12864-025-12492-y.