is there a good pipeline for the analysis of transposition using WGS data?
In other words, that is the procedure to assess whether a transposon has jumped between one sample and another?
I think you need to explain a bit more in detail what exactly it is you're looking for and what type of data you have.
A quick search in PubMed led to a couple of review papers on the subject -- have you perused those?
e.g. https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-015-0055-3, https://pubmed.ncbi.nlm.nih.gov/26025622/, https://pubmed.ncbi.nlm.nih.gov/26025622/, https://pubmed.ncbi.nlm.nih.gov/29390960/
These seem promising, I'll read them, thank you.
This seems like a very fitting (and very recent) publication, too:
"Mobile Genomics: Tools and Techniques for Tackling Transposons"
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