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
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written
by
d.chandanareddy.92 •
2 answers
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
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!
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written
by
maheshhbg •
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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?
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