Sorting The Scaffolds After Assembling

Question

[Javier Velazquez-Muriel]

Hi,

I am trying to process data from a bacterial genome after sequencing it using SOAPdenovo. I obtain a small number of scaffolds, and I would like, if possible, to guess their order in the genome. I happen to have the reference genome for the bacteria too, so I aligned the scaffolds to it using progressive Mauve, and they are spread over the genome. I was sort of expecting it. My question is: are there tools to guess the order when doing truly denovo assembling?

Answer 1

[Josh Herr]

I'm also in a similar situation where I have been trying to close contig gaps in a de novo genome sequencing project. I have a closely related genome and also used MAUVE. Have you used the MCM function (MAUVE contig mover)? My next recommendation would be to try to the PAGIT (Post Assembly Genome Improvement Toolkit) pipeline to rearrange contigs and close gaps.

[Javier Velazquez-Muriel]

Thanks, I will try that

Answer 2

[Lee Katz]

Mauve contig mover is one of the best out there because of its iterative approach. After that, there are several others out there. CONTIGuator has been one of my favorites because it plugs into a genome browser (ACT) and it also gives you good primer choices for closing gaps.

[Mehmet]

Hi,

I would like to ask you, how to replace scaffolds of the draft assembly based on matches with the reference assembly? I used MCM, and I checked that MCMC did not replace scaffolds of the draft assembly based on matches. For instance, scaffold 1 of reference assembly matched with scaffolds 116, 400, 340 of the draft assembly. what I want is to replace scaffold 116 as the first scaffold of the draft assembly.

How can I do that?