KILDA: identifying KIV-2 repeats from kmers

High concentration of lipoprotein(a) [Lp(a)], a lipoprotein with proatherogenic properties, is an important risk factor for cardiovascular disease. This concentration is mostly genetically determined by a complex interplay between the number of kringle IV type 2 repeats and Lp(a)-affecting variants. Besides Lp(a) plasma concentration, there is an unmet need to identify individuals most at risk based on their <i>LPA</i> genotype. We developed KILDA (KIv2 Length Determined from a kmer Analysis), a Nextflow pipeline, to identify the number of kringle IV type 2 repeats and Lp(a)-affecting variants directly from kmers generated from FASTQ files. The pipeline was tested on the 1000 Genomes Project (<i>n</i> = 2459) and results were equivalent to DRAGEN-LPA (<i>R</i> ²= 0.92). <i>In silico</i> datasets proved the robustness of KILDA's predictions under different scenarios of sequencing coverage and quality. In brief, KILDA is a robust, open-source, and free-to-use pipeline that can identify the number of kringle IV type 2 repeats and Lp(a)-associated variants even when inputting low-coverage libraries.