Re: [MUMmer-help] Exact alignment of contigs to a reference

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

Hi Ruth,
Unfortunately there is not an easy way to do this. The location of the
alignment gaps is contained in the .delta file, which you could parse to
create your mapping (the file format is described in the manual). Other
alternatives: If you only care about difference positions, the show-snps
program will report all SNPs and Indels w/ coordinates in both sequences.
Or the show-aligns will dump a textual alignment representation which you
could also parse.

Best,
-Adam


On Tue, May 5, 2015 at 4:59 PM, Miller, Ruth <Rut...@bc...> wrote:

> Hi,
>
> I have used NUCmer to align contigs I have generated from next-generation
> sequencing data to a reference.
>
> I would like to create a dictionary which contains the position of every
> base in the query contigs in the reference. I hoped I might be able to do
> this using the .coords file, however, although you can tell the start and
> end of every contig compared to the reference, it does not provide the
> positions of the gaps, so you cannot tell the exact alignment of each
> position in the query contig compared to the reference.
> Is there any way to get the exact details of the alignment using
> NUCmer/MUMmer, from which I could parse the 1:1 relationship of every
> position in the query contigs compared to the reference?
>
> Thanks,
>
> Ruth
>
>
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