Blackbird: structural variant detection using synthetic and low-coverage long-reads.

Overview

MOTIVATION: Recent benchmarks show that most structural variations, especially within 50-10,000 bp range cannot be resolved with short-read sequencing, but long-read structural variant callers perform better on the same datasets. However, high-coverage long-read sequencing is costly and requires substantial input DNA. Reducing coverage lowers cost but significantly impacts the performance of existing structural variation (SV) callers. Synthetic long-read technologies offer long-range information at lower cost, but leveraging them for SVs under 50 kbp remains challenging. RESULTS: × AVAILABILITY AND IMPLEMENTATION: Blackbird is available at https://github.com/1dayac/Blackbird.