finding contigs present in one assembly but missing from another

Question

[kallen83]

I have two pacbio assemblies for the same plant species, and I need to determine if there are regions represented in one assembly that are missing from the other. I have tried using progressiveMauve, and while I suspect that the information I'm looking for is somewhere in the output I'm having a hard time finding it.

Does anyone have a solution to this problem?

as an update, here are stats on one of the assemblies -- the other is similar to this.

number of contigs: 18355

mean contig size: 27903.8

median contig size: 15781

total size: 512174223

Pretty much every contig is big enough to include repetitive elements of some sort, so blastn output is not of much value.

[GenoMax]

It would be useful to add the size range of the contigs you have. Some of the solutions below may not be usable if you have large contigs. Using a program like LASTZ may be your best bet.

[Tm]

simplest approach is using tools like blastal/ blastN or blat for pairwise alignment, considering one assembly (assembly1) as query and another as database/subject (assembly2). Any contigs of assembly2 not showing hit as subject for assembly1 will be specific to assembly2.

[kallen83]

the complicating feature of that approach is repetitive elements missed by DUST and the relevant repetitive elements databases. At a first look it appears I'll need to build a repetitive element db for this species before I can proceed with something like that.

Answer 1

[colindaven]

I would use a bidirectional blastn program for this. You can predict ORFs and use blastx/blastp if looking at gene content (which might be easier for setting useful e-value cutoffs) or just use blastn. Long contigs will almost always tend to have hits with blastn though.

I have used proteinortho for this quite a lot in the past (at least at gene level). It creates a nice summary table.

Answer 2

[Antonio R. Franco]

Why don't you run a dotlet like program like those that are now being used for comparing a genome with an optical map ? I am refering to DAGChainer. Get the idea from this paper

[kallen83]

thanks, I'll have a look at that

Answer 3

[aindap]

Have you tried Assemblytics? You can use Mummer to align your two assemblies and then use Assemblytics to see the differences.