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

[Miller, R. <Rut...@bc...>]

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