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Percentage of similarity between two contigs files

Is there a way to show how much similarity/difference there is between two contigs.fasta files resulting from two different assemblers? I have already used QUAST, but I am looking for something that shows specifically how much difference there is between two results of different assemblers, where they differ, where they are similar, what percentage of similarity they have, etc.

assembly contigs
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updated by Ram Ram • written by ' '

2 answers

Indeed MUMmer could do the job. Have a look at the manual. Either extract your snps and indels from the delta file using provided mummerutilities. Or generate a MUMmerplot which will show large scale (dis)similarities. [ad] you can try to use them from our free galaxy.wur.nl interface.
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written by ALchEmiXt ALchEmiXt

Your online tool truly saved me so much value time. Thank you very much for your help.

I also wonder whether you know of any resources on how to interpret MUMmer plots? The official manual only has a little information merely on plots that result in a few long diagonal lines, and in my comparisons I have encountered plots containing a lot of dots, and I am wondering what that means. I have opened a different thread for that matter, in order not to go off-topic in this thread: How to interpret MUMmer plots? When do you know that your alignment was a good one?

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updated by Ram Ram • written by ' '

Sorry, late to the party. Depends how you run nucmer or promer. If you use the -maxmatch option it will report back any crossmatching sites. TO look into what these might be, you can convert the coords file to a BLAST crunch file (also at our galaxy instance if you like). That file can be used to visualize the MUMmer alignment in Artemis comparsion tool (ACT). Then you know exact what these dots represent (I guess repetitve elements).

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written by ALchEmiXt ALchEmiXt
Try Mauve or/and Mummer
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written by Antonio R. Franco Antonio R. Franco

I have already used MUMmer, which resulted in three files: (i) out.delta (ii) out.fil.delta (iii) out.fil.coords

Which of these should I look into? I believe that *.coords file is what I should look at, and probably the [% IDY] column in it?

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