Protocol to combine WGS with Nanopore for Structural Variant confirmation?

Question

[optimistsso4co3]

Hello everyone,

I'm reaching out to inquire if anyone is aware of a protocol or publication that delineates a methodology for integrating Illumina whole genome sequencing (WGS) data with long-read sequencing data from Nanopore technologies. Is there a recommended approach for this type of data fusion in the context of bioinformatics analysis?

[colindaven]

Please add more details, no one can help you without more info.

[dthorbur]

Hard to say if this fits, but you could make a consensus call among the two methodologies using a tool like SURVIVOR. However, this would be dangerous as long and short read data have different sensitivities to detect different classes of SV, so you may end up with a worse overall dataset by merging different sequencing techniques.

Answer 1

[trausch]

Maybe this helps: Nanopore sequencing of medulloblastoma. As part of this project, we added a long-read mode to delly so it supports now short- and long-reads which may help in these kind of projects. This preprint might also be helpful: MedRxiv