Tools that output positions of matching kmers

Question

[gil.hornung]

Hello community!

I am trying to find a tool that takes sequencing reads as input and a genome. The tools breaks the reads into kmers and outputs the positions of the kmers within the genome for each read. As this is a standard step in almost every aligner I'm hoping I can find some tool that does it without having to write it by myself.

[GenoMax]

As this is a standard step in almost every aligner

But it is an intermediate step that most users are not interested in and it is used as a seed for initial matches. While someone else may know of a tool that does what you want, you could create a new read with each k-mer and have the aligner output the CIGAR match for those fake reads,

Curious as to why you want to do this?

[gil.hornung]

Thanks, I thought there is a simpler and quicker option...