Tools to detect structural variation in PacBio "long" reads

Question

[Medhat]

There is some tools to detect PacBio long reads structure variations like:

parliament

Sniffles

multi-break

PBHoney

GATK "you need to change in GATK Best Practices"

my question If someone used any of them which is better or is there is any other tools?

Answer 1

[alwaysrejoice516]

Hi I am doing structural variation research in PacBio and just searched to your post. I checked the first three links and it looks like parliament is a combination of PBHoney and other SV detection tools which are analyzed illumina short reads data. Sniffles and PBHoney are specific to analyze SV in PacBio, and they are using different algorithm to detect SV, so it is hard to tell which is better. If i have time, I will try to compare them in the future, though. But maybe you can refer to this artical http://biorxiv.org/content/early/2016/12/09/092544

[Medhat]

actually the post is old and there is another tool that I did not mention multi-break

In general I would favour sniffle

[d-cameron]

There is also SMRT-SV as well now.

[alwaysrejoice516]

I know, just think this post is useful for me and wanted to give some response. one question, does Sniffle have published paper?

[Medhat]

To my knowledge he have only poster

[alwaysrejoice516]

Right, that's what I have seen.