Calling large structural variants from bacterial PacBio data

Question

[ThePresident]

Hello,

I am trying to analyse genomic structural variants (large inversions, deletions rearrangements - not small SNPs/InDels) in bacterial clonal populations. I have some evidence that my organism of interest is "experiencing" such structural variations, however the frequency might be relatively small. I was wondering if long-read sequencing like PacBio might be able to identify such variants compared to a reference strain?

From my understanding of PacBio chemistry this should be possible, however I am wondering if there are any tools currently available for this?

Thanks,

TP

Answer 1

[Medhat]

short answer yes it can, regarding tools there are two of them Sniffles and PBSuite

you can read here also Tools to detect structural variation in PacBio "long" reads

[ThePresident]

Thanks, that's what I was looking for.