How to determine insert location in genome using WGS data?

Question

[DrAcula]

Hello!

My knowledge is limited to using RNAseq libraries for analysis be it bulk or sn/sc. However, I want to also learn how to handle WGS data so for starters have a small challenge that I would like to complete.

I have inserted a sequence of DNA approx ~8KB long into a genomic locus of a cell line of human origin using CrisprCas9, which I know is there by virtue of qualitative PCR. Now we have performed whole-genome sequencing to validate that there were no off-target insertions in alternative non-specific sites of the genome. My understanding is that this will be a combination of refrence based assembly and de novo assembly to align A) ref human genome and B) targetted/inserted DNA.

What pipeline can I use to perform this analysis? Can you please point me towards a step-by-step vignette?

Thanks a lot for your help!

[GenoMax]

Past threads that may be of interest
Identification of the sequence insertion site in the genome
detecting insertion sites of transgene in mouse genome

[DrAcula]

Thanks GenoMax, I will take a read and get back to this thread with an update.