Orientation of flanking sequences neighboring to insertions in long reads

Understanding three-dimensional chromatin organization in diploid genomes - Computational and Structural Biotechnology Journal

Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis, BMC Genomics

Targeted Long‐Read Sequencing Identifies a Retrotransposon Insertion as a Cause of Altered GNAS Exon A/B Methylation in a Family With Autosomal Dominant Pseudohypoparathyroidism Type 1b (PHP1B) - Miller - 2022 - Journal

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements - ScienceDirect

PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads, Genome Biology

IJMS, Free Full-Text

Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

Long-read human genome sequencing and its applications

Strand asymmetries across genomic processes - Computational and Structural Biotechnology Journal

Detection of trait-associated structural variations using short-read sequencing - ScienceDirect

A pipeline for complete characterization of complex germline rearrangements from long DNA reads, Genome Medicine