Question: Find structural variants comparing two assemblies
1
gravatar for crimsontabaq
12 months ago by
crimsontabaq50
Russia, Kazan
crimsontabaq50 wrote:

Is there a rapid way of comparing two large assemblies quantitatively, like generating a file with all large structural variants, or SV - gaps, inversions, etc., and theirs coordinates? The idea is basically to find out what one assembler particularly failed to assemble, compared to another one. Not using reads but assemblies alone, e.g. by breaking one of them on small pieces and use them as pseudo-reads.

There are ways of comparing assemblies, but they are not precise (e.g. dotplot, just visualizes but doesn't provide number and type of SV) and are finite (e.g. GMASS score or likehood test) - one cannot analyze what is different, but just HOW different.

This is simple task and quite typical for evaluation of assemblers' output, but I couldn't find any working solution. GATK finds only small SVs and poor at finding inversions, mummer's show-diff has the same problems + running two long on large genomes.

ADD COMMENTlink modified 12 months ago • written 12 months ago by crimsontabaq50
1

You could combine something like aligning the de-novo contigs to your reference with minimap2 and then using https://github.com/eldariont/svim

ADD REPLYlink written 12 months ago by cmdcolin1.4k
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