Question: Calling large structural variants from bacterial PacBio data
0
gravatar for ThePresident
2.7 years ago by
ThePresident120
ThePresident120 wrote:

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

pacbio sv • 931 views
ADD COMMENTlink modified 2.7 years ago by Medhat8.4k • written 2.7 years ago by ThePresident120
3
gravatar for Medhat
2.7 years ago by
Medhat8.4k
Texas
Medhat8.4k wrote:

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

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Medhat8.4k

Thanks, that's what I was looking for.

ADD REPLYlink written 2.7 years ago by ThePresident120
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