Assessing Repeat Content Among Assembled Contigs

Question

[Abhi]

Hi All

I am trying to asses and compare genomes assemblies for the same data set and suspect there can be some contigs assembled which are overlapping in the genome region they cover.

So wondering if I can detect and visualize these differences. In essence what I would like to do a given a multi-fasta file, do a pariwise comparison between all the contigs and see how many contigs have common regions from the genome.

PS: I have asked somewhat similar question but this time this is more specific.

http://biostar.stackexchange.com/questions/13370/comparing-multiple-genome-assemblies-with-reference

Thanks! -Abhi

Answer 1

[Torst]

You should be able to use nucmer from the MuMMer package to do this, using your contigs multifasta file as the Query and as the Subject and using --nosimplify option. You can then visualize the dotplot using mummerplot to get a feel for the repetitiveness, then formally using the mummer output files.