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Updated: Sep 11, 2025

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Detecting Foldback Artifacts in Long-reads.

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

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

Biorxiv : the Preprint Server for Biology

|August 12, 2025

Summary

This summary is machine-generated.

A new tool, Breakinator, identifies foldback artifacts in long-read sequencing data, improving the accuracy of structural variation detection. This open-source software flags problematic reads, reducing false positives in genomic analyses.

Keywords:

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

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Last Updated: Sep 11, 2025

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Long-read sequencing technologies are crucial for identifying complex structural variations in genomes.
Technical artifacts in sequencing data can lead to inaccurate structural variant (SV) calls.
Existing quality control tools may not detect all types of sequencing artifacts.

Purpose of the Study:

To develop an open-source tool, Breakinator, for detecting foldback artifacts in long-read sequencing data.
To identify and flag previously known chimeric artifacts in addition to foldbacks.
To improve the accuracy of structural variation detection by reducing false positives.

Main Methods:

Developed an alignment-based approach for artifact detection.
Created the open-source tool Breakinator to flag putative artifact reads.
Profiled artifact occurrences across diverse sequencing conditions.

Main Results:

Breakinator successfully flags putative foldback artifact reads.
The tool detects artifacts that are missed by existing quality control methods.
Foldback and chimeric read occurrences were profiled across various sequencing platforms (Nanopore, SMRT), specimens, and library preparations.

Conclusions:

Breakinator enhances the reliability of long-read sequencing data analysis.
The tool addresses a gap in quality control for detecting specific technical artifacts.
Accurate artifact detection is essential for robust structural variation calling in genomics.