Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

We sequenced the genome of the Yoruban reference individual NA19240 on the long read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, and a comparison with the performance of structural variant calling from short read sequencing data. The structural variant caller Sniffles after NGMLR or minimap2 alignment provides the most accurate results, but additional confidence or sensitivity can be obtained by combination of multiple variant callers. Sensitive and fast results can be obtained by minimap2 for alignment and combination of Sniffles and SVIM for variant identification. We describe a scalable workflow for identification, annotation, and characterization of tens of thousands of structural variants from long read genome sequencing of an individual or population. By discussing the results of this well-characterized reference individual we provide an approximation of what can be expected in future long read sequencing studies aiming for structural variant identification.