kGWASflow is a Snakemake pipeline developed for performing k-mers-based genome-wide association study (GWAS) based on the method developed by Voichek et al. (2020). It performs several pre-GWAS analysis including read trimming, quality control and k-mer counting. It implements the kmersGWAS method worfklow for performing k-mers-based GWAS. The pipeline also contains post-GWAS analysis, such as finding and aligning the source reads for k-mers, aligning kmers and source reads to a reference genome.