This document summarizes methods for improved structural variant (SV) detection and interpretation from long-read sequencing data. It describes: 1. A breast cancer study using 75x PacBio coverage that detected SVs through alignment, copy number analysis, and assembly-based variant calling. 2. Tools the author has developed or improved for long-read SV analysis including NextGenMap-LR for alignment, Sniffles for SV detection, and SplitThreader for SV interpretation. 3. How the author's approaches offer more accurate SV detection over existing methods by improving alignments and detection algorithms as well as enabling assembly-guided analysis and reconstruction of complex cancer genome rearrangements.