Question: Tools to detect structural variation in PacBio "long" reads
2
gravatar for Medhat
2.8 years ago by
Medhat8.2k
Texas
Medhat8.2k wrote:

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?

snp sequence genome • 1.9k views
ADD COMMENTlink modified 2.2 years ago • written 2.8 years ago by Medhat8.2k
0
gravatar for alwaysrejoice516
2.2 years ago by
US/NJ
alwaysrejoice5160 wrote:

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

ADD COMMENTlink written 2.2 years ago by alwaysrejoice5160

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

In general I would favour sniffle

ADD REPLYlink written 2.2 years ago by Medhat8.2k

There is also SMRT-SV as well now.

ADD REPLYlink written 2.2 years ago by d-cameron2.0k

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

ADD REPLYlink written 2.2 years ago by alwaysrejoice5160

To my knowledge he have only poster

ADD REPLYlink written 2.2 years ago by Medhat8.2k

Right, that's what I have seen.

ADD REPLYlink written 2.2 years ago by alwaysrejoice5160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 687 users visited in the last hour