Detecting foldback artifacts in long-reads
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.
Fields of Study & Subjects
Machine Learning in Materials Science
Protein Structure and Dynamics
Genomics and Phylogenetic Studies
Publication details
- Journal / source
- BMC Genomics
- Publisher
- Springer Science and Business Media LLC
- Volume
- 27
- Issue
- 1
- Pages
- 144–144
- Publication date
- 7 January 2026
- Language
- EN