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

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 va...

Descripción completa

Detalles Bibliográficos
Autores principales: Fletcher, Kyle, Zhang, Lin, Gil, Juliana, Han, Rongkui, Cavanaugh, Keri, Michelmore, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8061198/
https://www.ncbi.nlm.nih.gov/pubmed/33883006
http://dx.doi.org/10.1186/s13059-021-02326-x
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02326-x.

Ejemplares similares