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

doi:10.1186/s13059-021-02326-x

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

Genome Biol. 2021 Apr 21;22(1):115. doi: 10.1186/s13059-021-02326-x.

Authors

Kyle Fletcher¹, Lin Zhang¹, Juliana Gil¹, Rongkui Han¹, Keri Cavanaugh¹, Richard Michelmore^{2

3}

Affiliations

¹ The Genome Center, University of California, Davis, USA.
² The Genome Center, University of California, Davis, USA. rwmichelmore@ucdavis.edu.
³ Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, USA. rwmichelmore@ucdavis.edu.

Abstract

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.

Keywords: Arabidopsis; Bremia; GBS; Genetic map; Genotype-by-sequencing; K-mer; Lettuce; Oomycete.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amplified Fragment Length Polymorphism Analysis / methods*
Arabidopsis / genetics
Chromosome Mapping
Computational Biology / methods*
Exome Sequencing
Genetic Linkage*
Genome, Plant
Genomics / methods*

Grants and funding

S10 OD010786/OD/NIH HHS/United States