AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.
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ABSTRACT:
SUBMITTER: Fletcher K
PROVIDER: S-EPMC8061198 | biostudies-literature | 2021 Apr
REPOSITORIES: biostudies-literature
Publications
AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.
Fletcher Kyle K Zhang Lin L Gil Juliana J Han Rongkui R Cavanaugh Keri K Michelmore Richard R
Genome biology 20210421 1
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 ...[more]
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