Failure to Map

[YianniL]

Hi,

I'm really interested in using graphmap for doing some Nanopore alignments with predicted sequences but I can not seem to get an alignment. I tried to get an alignment with a simple sequence just to test it out, but I am not successful. For example:

Say I have dog.fasta like this:
>dog
ATC

And ref.fasta like this:
>dog
ATCG

I am getting 0 mapped reads. Even when I try to align ref.fasta to itself I am getting 0 mapped reads.
This is the command I'm running:

graphmap align -r ref.fasta -d dog.fasta -o output.sam

Any help would be greatly appreciated because we really want to use graphmap for our alignments.
Thanks for your time!

Best,
YianniL

[ghost]

It might be that your sequences are just too short and the algorithm does not find any seeds (anchors?) to do the alignment. Make the example a bit longer about 20 to 30 nt...
Hope I am right with this. Don't know the algo. in detail.