how to assemble scaffolds to chromosome??

Question

[d.chandanareddy.92]

Hi

I have NGS data of Anopheles quadriannulatus assembled till scaffold level. I used software MUMmer to get alignment of the scaffolds to the reference chromosome. Now I have scaffolds and their respective coordinates on the reference chromosome. I would like to know if there is a software/tool to assemble these scaffolds to chromosome.

Thank you

[iraun]

I don't understand at all your question, if you have allready the chromosomes why are you trying to assemble scaffolds? I mean, you want to order your scaffolds or something like that?

[d.chandanareddy.92]

I have reference chromosome ie, chromosome of Anopheles gambiae. I want to assemble the scaffolds of Anopheles quadriannulatus using the reference chromosome . I do not have the chromosome data of Anopheles quadriannulatus.

Thank you

Answer 1

[iraun]

You can only assemble scaffolds if there is sufficient mapping information (Genetic Maps, Optical mapping..). Many genome assemblies are only assembled to the scaffold level, so I think that in general (I don't know for your case) you can work with the scaffolds. The only think that you can do (since you have a closely related specie) is classify your scaffolds:

• Placed scaffolds: the scaffolds have been placed within a chromosome.
• Unlocalized scaffolds: although the chromosome within which the scaffold occurs is known, the scaffold's position or orientation is not known.
• Unplaced scaffolds: it is not known which chromosome the scaffold belongs to.

You can create AGP files (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml) containing all the information about the relationship between contigs, scaffolds and chromosomes.

Hope it helps

Answer 2

[maheshhbg]

Hi

You can use a tool called ABACAS for this purpose.

typical usage would be:

perl abacas.1.3.1.pl -r reference_genome.fa -q contigs.fa -p nucmer -N -m -b

thank you!