A faster implementation of association mapping from k-mers

Genome wide association studies (GWAS) attempt to map genotypes to phenotypes in organisms. This is typically performed by genotyping individuals using microarray or by aligning whole genome sequencing reads to a reference genome. Both approaches require knowledge of a reference genome which limits their application to organisms with no or incomplete reference genomes. This caveat can be removed using alignment-free association mapping methods based on k-mers from sequencing reads. Here we present an implementation of an alignment free association mapping method [1] to improve its execution time and flexibility. We have tested our implementation on an E. Coli ampicillin resistance dataset and observe improvement in performance over the original implementation while maintaining accuracy in results. Finally, we demonstrate that the method can be applied to find sex specific sequences.