k mdiff, large-scale and user-friendly differential k-mer analyses.

Abstract

Genome wide association studies elucidate links between genotypes and phenotypes. Recent studies point out the interest of conducting such experiments using k-mers as the base signal instead of single-nucleotide polymorphisms. We propose a tool, kmdiff, that performs differential k-mer analyses on large sequencing cohorts in an order of magnitude less time and memory than previously possible. https://github.com/tlemane/kmdiff. Supplementary data are available at Bioinformatics online.