Re: [MUMmer-help] delta-filter parameters

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

Hi Helene,
-r and -q are not necessarily equivalent to -g. Here's a little more detail:

-m is equivalent to the union of alignments found by running both -r and -q
separately

-1 is the equivalent of the intersection of alignments found by running
both -r and -q separately

-g is best though of as a global alignment. All alignments will be
consistently ordered in both the reference and query, and no inversions are
allowed.

For what it's worth, I typically use -m for genome comparisons (because it
preserves paralogous alignments), and -q for mapping reads or contigs to a
reference (because it will allow for structural variants).

Best,
-Adam


On Wed, Jan 28, 2015 at 3:45 AM, Hélène Chiapello <
hel...@to...> wrote:

> Hello
>
> I used nucmer to align pair of closed bacteria genomes.
> I have a question regarding delta-filter parameters:
> are the "-r -q" and "-g" options equivalent ?
> My undersanding is that the "-g" option assumes collinear
> genomes and do not allow for inversion and translocation,
> while the "-r -q" option allow one to one mapping with possible
> "local" inversions.
> Is that correct ?
>
> Thanks in advance
>
> Helene
>
>
>
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