Question: how to assemble scaffolds to chromosome??
gravatar for d.chandanareddy.92
6.1 years ago by
d.chandanareddy.920 wrote:


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.


next-gen assembly • 6.1k views
ADD COMMENTlink modified 6.0 years ago by maheshhbg20 • written 6.1 years ago by d.chandanareddy.920

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?

ADD REPLYlink written 6.1 years ago by iraun3.8k

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. 


ADD REPLYlink written 6.1 years ago by d.chandanareddy.920
gravatar for iraun
6.1 years ago by
iraun3.8k wrote:

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 ( containing all the information about the relationship between contigs, scaffolds and chromosomes.

Hope it helps

ADD COMMENTlink written 6.1 years ago by iraun3.8k
gravatar for maheshhbg
6.0 years ago by
maheshhbg20 wrote:


You can use a tool called ABACAS for this purpose.

typical usage would be:

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

thank you!

ADD COMMENTlink modified 13 months ago by _r_am31k • written 6.0 years ago by maheshhbg20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1194 users visited in the last hour