SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Improve fragmented genome assembly with PacBio? BasVerb De novo discovery 4 02-08-2016 06:25 AM
PBcR hybrid assembly of 6.5MB genome with PacBio and MiSeq DrSpace Bioinformatics 9 06-11-2015 12:40 PM
Pacbio releases Arabidopsis genome assembly dataset pacbio Pacific Biosciences 1 09-05-2013 07:23 PM
Have a genome assembly, what should I do with 15x Pacbio reads? lemur2 Pacific Biosciences 2 10-25-2012 09:06 PM

Reply
 
Thread Tools
Old 10-28-2016, 03:20 AM   #1
carlos
Junior Member
 
Location: Spain

Join Date: Feb 2008
Posts: 7
Default Pacbio assembly of polymorphic genome

Hi guys,

a quick question. I am new to pacbio. I've just received pacbio data for assembling a genome (low coverage). It comes from a highly polymorphic genome. What is the most suitable assembler that would handle pacbio and that would let me also keep the two haplotypes separeted?

Best regards,

Carlos
carlos is offline   Reply With Quote
Old 10-28-2016, 08:07 AM   #2
gconcepcion
Member
 
Location: Menlo Park

Join Date: Dec 2010
Posts: 68
Default

Quote:
Originally Posted by carlos View Post
Hi guys,

a quick question. I am new to pacbio. I've just received pacbio data for assembling a genome (low coverage). It comes from a highly polymorphic genome. What is the most suitable assembler that would handle pacbio and that would let me also keep the two haplotypes separeted?

Best regards,

Carlos
With low coverage data, you will barely be able to assemble a decent un-separated (haploid) assembly. Typically we recommend about 60X coverage for haploid assembly, and twice that for diploid assembly, or else won't have enough coverage to sufficiently resolve both haplotypes

What does "Low coverage" equate to?

That said, FALCON or Canu are your best options at this point.

Last edited by gconcepcion; 10-28-2016 at 08:10 AM.
gconcepcion is offline   Reply With Quote
Old 10-28-2016, 08:17 AM   #3
carlos
Junior Member
 
Location: Spain

Join Date: Feb 2008
Posts: 7
Default

Quote:
Originally Posted by gconcepcion View Post
With low coverage data, you will barely be able to assemble a decent un-separated (haploid) assembly. Typically we recommend about 60X coverage for haploid assembly, and twice that for diploid assembly, or else won't have enough coverage to sufficiently resolve both haplotypes

What does "Low coverage" equate to?

That said, FALCON or Canu are your best options at this point.
Hi,

10X, I wanted to say to help the assembly (scaffolding instead of denovo). I would like to use it for scaffolding in a diploid way.

Regards
carlos is offline   Reply With Quote
Old 10-28-2016, 09:07 AM   #4
gconcepcion
Member
 
Location: Menlo Park

Join Date: Dec 2010
Posts: 68
Default

Quote:
Originally Posted by carlos View Post
Hi,

10X, I wanted to say to help the assembly (scaffolding instead of denovo). I would like to use it for scaffolding in a diploid way.

Regards
If you can shed some light on what you are trying to do, and what data you have to start with, it will make it easier for people to help you.

Now I understand that you are trying to scaffold short read data, and not perform Denovo assembly of low coverage pacbio data alone. How much short read data do you have? How large is the genome? What evidence do you have that the genome is highly polymorphic? Do you already have a short read assembly? How does it look?

To my knowledge, there are no current tools available for scaffolding short read assemblies with (extremely) low coverage pacbio data resulting in diploid assemblies.
gconcepcion is offline   Reply With Quote
Reply

Tags
assembler, heterozygosity, pacbio, polymorphism

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO