We (pluralis maiestatis) have developed a worfklow/pipeline to identify, annotate and visualize structural variation from long read sequencing data (Oxford Nanopore and PacBio).
This is based on Snakemake and can be found on GitHub: https://github.com/wdecoster/nano-snakemake
Integrated are recently developed aligners (minimap2 and ngmlr) and specific variant callers (sniffles, nanosv and npInv). More information about this can also be found in our preprint on structural variants in NA19240 PromethION data.
All feedback and contributions are welcome!