Re: [MUMmer-help] whole genome alignment question

[Adam P. <aph...@gm...>]

Hi Diogo,
If you run the 'dnadiff' script that comes with MUMmer it will generate a
.report file that will include global similarity metrics based on Nucmer
alignments.

Best,
-Adam


On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <dio...@gm...>
wrote:

> Hi,
>
> This is a very naive, simple question, but I can’t seem to locate a good
> answer for it on the manual.  I have a set of bacterial genomes that I want
> to align against a different (single) bacterial genome.  The obvious tool
> to do this seems to be NUCmer and I did a test run of 1 genome against the
> “reference” genome by doing:
>
> nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>
>
> NUCmer runs fine and when I do show-coords I get the table with the
> alignments and the respective identity between the 2 genomes I am
> comparing.  But what I would like would be to get a single, global, percent
> identity score between the 2 genomes, as I basically want to compare the
> two genomes at a global level.  Is there a simple way to do this using the
> MUMer suite?
>
> Many thanks!
>
>
> Best,
> d.
>
>
>
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
>
>
>
>
>
>
>
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