mapping kmers with bwa

If you used smudgeplot extract to extract a fasta file with kmers you might also want to locate them in the genome. This process is just a tweaked read mapping, because we desire to locate only the kmers to their exact matches.

Before providing the solution, I would like to thank Daniel Standage for giving me this solution.

With following bwa mem setting, the extracted kmers will be located in the assembly:

bwa mem -k 21 -T 21 -a -c 5000 assembly.fasta your-21mers.fasta

We assume here you are familiar with bwa mem, if not, we recommend to look up a different tutorial first.