TY - JOUR T1 - AFLAP: Assembly-Free Linkage Analysis Pipeline using <em>k</em>-mers from whole genome sequencing data JF - bioRxiv DO - 10.1101/2020.09.14.296525 SP - 2020.09.14.296525 AU - Kyle Fletcher AU - Lin Zhang AU - Juliana Gil AU - Keri Cavanaugh AU - Richard Michelmore Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/09/15/2020.09.14.296525.abstract N2 - Background Genetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has led to the production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly of the organism under study, or a close relative, to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers. This removes potential biases including preferential read alignment and variant calling.Results We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers specific for each parent contained over 130,000 markers that were concordant with the genomic assembly of the five chromosomes. AFLAP was then applied to 83 F1 individuals, sequenced to &gt;5x coverage, generated from two crosses of the oomycete Bremia lactucae. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. The genetic map was used to fragment, order, orient, and scaffold the reference assembly of B. lactucae, resulting in a much improved, genetically consistent genome assembly.Conclusions AFLAP can therefore be used to generate high density linkage maps and improve draft genome assemblies of non-model organisms when a mapping population sequenced to adequate coverage is available. The genetic maps produced for B. lactucae were accurately aligned to the reference assembly and resulted in significant improvements of the assembly.Competing Interest StatementThe authors have declared no competing interest. ER -