Pacbio assembly of polymorphic genome

[carlos]

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

[gconcepcion]

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.

[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.

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

[gconcepcion]

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.