Re: [MUMmer-help] A clarification about NUCmer

[Govinda K. <gk...@be...>]

Hi Adam,

Thanks for the quick response. It helps a lot.

Regards,
Govinda.


On 6 February 2014 08:12, Adam Phillippy <aph...@gm...> wrote:

> 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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>