I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome alignment, and I am trying to reorder scaffolds according the mummer result. But I found it's too complicated to do this by myself, many scaffolds may align to multiple Oryza sativa Japonica chromosomes or multiple loci in the same chromosome.
What software can I use to handle this task?
I've been using ATAC to successfully align different versions of the rice genome assembly. There is a chance it will work for you between two closely related species (potato and tomato work well for example).
It's not massively user friendly, but it's very fast, and it produces long, 'clean' alignments (i.e. almost all 1 to 1 alignments). The output format is a bit cryptic (zero-based start position and length instead of the more usual 1-based start and end positions), but as I said, it should basically output the order for you in about 30 minutes.
Have you tried Mauve alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres one I use when in need.
Mauve contains a function called Mauve Contig Mover (MCM) which can be used to a) compare an assembly to a reference and/or b) rearrange contigs to improve assembly quality.
I use the tutorial as above which uses the GUI for Mauve. I
