Re: [MUMmer-help] Aligning a 30 Mb scaffold to a 3 Gb Reference

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

Hi Sanjit,
The best parameters depend on how related your scaffold is to the reference
assembly (same genome / species?) and how fragmented your contigs are.
Nucmer will not align through large stretches of N's, so if your scaffold
consists of a fasta file with contigs separated by N's, you will get
fragmented alignments as a result. As I suggested previously, I would run
delta-filter to select the best alignments for your scaffold versus the
reference genome. Then, from inspecting the coordinates of the remaining
matches you should be able to determine the extents of your scaffold mapped
to the reference.

-c 100 is relatively small, so for a 3GB genome, you will get a large
number of repeat-induced matches. If you are dealing with the same species,
I would increase -l to 50, and -c to your minimum contig size (say between
1000 or 5000), and increase the -g parameter to a few hundred.

Best,
-Adam


On Mon, Apr 27, 2015 at 1:32 PM, Sanjit Singh Batra <san...@gm...>
wrote:

> Hi!
>
> I asked this question as a response to the show-tilling thread, as you
> suggested. Although they are unrelated, it would be great to hear any
> suggestions from you regarding this. Any help with this problem will
> greatly reduce my computational off-time.
>
> Thanks again!
> sanjit
>
> On Tue, Apr 21, 2015 at 10:31 AM, Adam Phillippy <aph...@gm...>
> wrote:
>
>> Hi,
>> I see I picked up a separate question you had regarding show-tiling,
>> happy to answer questions in that more recent thread if you have further
>> questions.
>>
>> Best,
>> -Adam
>>
>>
>> On Fri, Apr 10, 2015 at 5:00 AM, Sanjit Singh Batra <
>> san...@gm...> wrote:
>>
>>> Hey!
>>>
>>> I have a 30Mb scaffold that was assembled using optical maps. I would
>>> like to align it to a 3Gb long reference assembly. Given the method through
>>> which this scaffold was constructed, it should align to a region in the
>>> reference, roughly the same size as itself.
>>>
>>> I am currently running nucmer with the -c 100 flag, and I get a very
>>> large number of fragmented alignments, the longest of which is under 1Mb.
>>> Is there any way I can alter the flags to get a larger, less fragmented
>>> alignment, for this particular case?
>>>
>>> Any suggestions are appreciated. Thanks!
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>>> Develop your own process in accordance with the BPMN 2 standard
>>> Learn Process modeling best practices with Bonita BPM through live
>>> exercises
>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
>>> event?utm_
>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>
>>>
>>
>