Simple scaffolding problem

[jmartin]

I have a collection of genomic contigs that I want to scaffold using a closely related species' genomic reference as the backbone. I just want to use the reference to orient and space the contigs, and then fill in gaps with Ns. What would be the best (and simplest) way to accomplish that?

[SES]

ABACUS was designed for ordering contigs relative to a reference, and with IMAGE you can fill the gaps with your reads. Both programs are a part of the PAGIT pipeline. In my experience, ABACUS is quite straightforward to use but IMAGE is very buggy; it will change the name of you input files, create lots of temporary files and fail without clear warnings. Also, I recall having to change some of the code with IMAGE to get it working correctly.

[flxlex]

Maybe Mauve Contig Mover can help?

[Stroehli]

Scaffold_builder (http://www.scfbm.org/content/8/1/23) looks straight-forward and could be a good tool for that purpose. Haven't had the time to test it myself yet though.