I am assembling a genome from an organism that we can't cultivate. We don't know if we sequenced multiple strains or one strain which is polymorphic. Anyway, the point is when I get the assemblies from Abyss, Ray and SOAP-denovo, I always get a high redundancy; by redundancy I mean that there are long sequences (in one of the assemblies up to 45000nt) that have been placed by the algorithm in multiple scaffolds. Now I see there is at least one software for reducing this (Simplifier) but I don't think it is ok to use in this situation. I would like to choose the assembly characterized by the minimum redundancy. How can I "measure" redundancy? Someone used the total number of non-self alignments exhibited by scaffolds, but this does not inform on the extent of those alignments. At the same time, the total number of nucleotides in those alignments would provide this information but will not tell how many of the scaffolds contain redundant sequences.
There are several possibilities:
You can do a repeat annotation (REPET pipeline, RepeatModeler) und use RepeatMasker to tell you the proportion of the genome that is redundant.
Alternatively, there is a tool that directly measures the redundany using
suffix trees. It could be that for large genomes you need a lot of memory.
See: http://guanine.evolbio.mpg.de/cgi-bin/ir/ir.cgi.pl
The corresponding paper is the following:
B. Haubold and T. Wiehe. How repetitive are genomes? BMC Bioinformatics, 7:541, 2006.
Sorry for the late reply Youssar. Can't say. Anyway, it is not a matter of repeats, there are redundant parts in my assembly that are 20k long and contain genes and so on. I think is caused by the heterogeneous DNA we sequenced, e.g. multiple and genetically different individuals. We will see.
Sorry, maybe I am not clear. I have the tools to assess the redundancy. What I would like to know is if there are accepted measures to quantify it.
You can judge redundancy sequence by two evidence ,firstly, you can judge by self-alignment with lastz ,because redundancy are very similar .secondly ,judge by sequence depth from the short read aligning to your genome assembly,because for a diploid,redundancy shared the mapping reads.
you can find how to do it in oyster genome paper or heliconious genome paper.
Is it possible to make this redundant part circular? Maybe You have an extrachromosomal part of the genome, like a plasmid? Then a high redundancy of this part would be quite obvious...
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