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

Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved with short-read sequencing, but long-read SV callers achieve great results on the same datasets. While improvements have been made, high-coverage long-read sequencing is associated with higher costs and input DNA requirements. To decrease the cost one can lower the sequence coverage, but the current long-read SV callers perform poorly with coverage below 10×. Synthetic long-read (SLR) technologies hold great potential for structural variant (SV) detection, although utilizing their long-range information for events smaller than 50 kbp has been challenging.

In this work, we propose a hybrid novel integrated alignment- and local-assembly-based algorithm, Blackbird, that uses SLR together with low-coverage long reads to improve SV detection and assembly. Without the need for a computationally expensive whole genome assembly, Blackbird uses a sliding window approach and barcode information encoded in SLR to accurately assemble small segments and use long reads for an improved gap closing and contig assembly. We evaluated Blackbird on simulated and real human genome datasets. Using the HG002 GIAB benchmark set, we demonstrated that in hybrid mode, Blackbird demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5× coverage to achieve F1 scores (0.835 and 0.808 for deletions and insertions) similar to PBSV (0.856 and 0.812) and Sniffles2 (0.839 and 0.804) using 10× Pacbio Hi-Fi long-read coverage.