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

By Wouter De Coster, Arne De Roeck, Tim De Pooter, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Kristel Sleegers, Christine Van Broeckhoven

Posted 03 Oct 2018
bioRxiv DOI: 10.1101/434118 (published DOI: 10.1101/gr.244939.118)

We sequenced the Yoruban NA19240 genome on the Oxford Nanopore PromethION for benchmarking and evaluation of recently published aligners and structural variant calling tools. In this work, we determined the precision and recall, present high confidence and high sensitivity call sets of variants and discuss optimal parameters. The aligner Minimap2 and structural variant caller Sniffles are both the most accurate and the most computationally efficient tools in our study. We describe our 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 genome we provide an approximation of what can be expected in future long read sequencing studies aiming for structural variant identification.

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