Question: finding contigs present in one assembly but missing from another
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gravatar for kallen83
2.7 years ago by
kallen8310
kallen8310 wrote:

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.

alignment assembly genome • 802 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by kallen8310
1

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax89k

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.

ADD REPLYlink written 2.7 years ago by toralmanvar900

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.

ADD REPLYlink written 2.7 years ago by kallen8310
1
gravatar for colindaven
2.7 years ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:

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.

ADD COMMENTlink written 2.7 years ago by colindaven2.3k
1
gravatar for Antonio R. Franco
2.7 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

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

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Antonio R. Franco4.5k

thanks, I'll have a look at that

ADD REPLYlink written 2.7 years ago by kallen8310
0
gravatar for aindap
2.7 years ago by
aindap120
United States
aindap120 wrote:

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

ADD COMMENTlink written 2.7 years ago by aindap120
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