AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh, Richard Michelmore

Research output: Contribution to journalArticlepeer-review


Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

Original languageEnglish (US)
Article number115
JournalGenome Biology
Issue number1
StatePublished - Dec 2021


  • Arabidopsis
  • Bremia
  • GBS
  • Genetic map
  • Genotype-by-sequencing
  • K-mer
  • Lettuce
  • Oomycete

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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