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. Competing Interest Statement M.M. holds equity in Bayer, Delve Bio, Isabl, and Karyoverse; consults for Delve Bio; receives research funding from Bayer; and receives patent licensing payments from Bayer and Labcorp. Footnotes Updated our method, Breakinator, to support the more common SAM/BAM/CRAM format files along with PAF files, highlighted that sequence between aligning read segments in artifact reads is enriched for repetitive elements, and added a paragraph discussing the envisioned use case of Breakinator in an analysis pipeline depending on sample and datatype.