Re: [MUMmer-help] A clarification about NUCmer

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

Hi Govinda,
There is no minimum percent identity threshold for Nucmer and no guarantees
on what it will find. Instead, the sensitivity and quality of the
alignments depends on the minimum match size and cluster parameters chosen.
The closest thing to an identity threshold are the dynamic programming
extension scores, which are set to +3/-7. This equates to a min avg
identity of 70% for the DP algorithm to continue extending. However, Nucmer
will rarely find these low identity alignments, because they will likely
not be seeded. With default parameters, Nucmer is generally sensitive to
alignments >90% idy.

If you want to cap the alignments to a certain identity, after the fact,
you can run delta-filter with the -i option to filter alignments below your
desired threshold.

Hope this helps,
-Adam



On Tue, Feb 4, 2014 at 3:32 PM, Govinda Kamath <gk...@be...> wrote:

> Hi,
>
> In NUCmer, what is the default percent identity threshold, above which
> results are reported in the out.delta file? Also what is the metric (like
> Hamming distance or Edit distance) is this calculated in?
>
> Thanks,
> Govinda.
>
>
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