Richard Finkers

Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

This paper presents a method for haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data, achieving high-quality chromosome-level assemblies with haplotype-specific resolution.

Chromosome-scale genome assemblies of five different Brassica oleracea morphotypes provide insights in intraspecific diversification

The paper presents chromosome-scale genome assemblies for five Brassica oleracea morphotypes and analyzes their structural variations and evolutionary dynamics.

De novo whole-genome assembly of Chrysanthemum makinoi, a key wild ancestor to hexaploid Chrysanthemum

This paper presents a high-quality de novo genome assembly of Chrysanthemum makinoi, a wild diploid ancestor of cultivated chrysanthemums, using long-read and short-read sequencing technologies.

Insights from the first genome assembly of Onion (Allium cepa)

The paper presents the first high-quality genome assembly of onion, revealing a large genome with extensive transposon content and a high number of putative gene models.

Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

This paper introduces PopPoly, a method for estimating polyploid haplotypes and improving genotype dosage in F1-populations using short sequence reads and pedigree information.

Haplotype assembly of autotetraploid potato using integer linear programming

This paper develops an integer linear programming method for haplotype assembly in autotetraploid potato, showing improved accuracy over existing methods on both simulated and real data.

TriPoly: a haplotype estimation approach for polyploids using sequencing data of related individuals

TriPoly improves haplotype estimation in polyploids using parent-offspring trios and Mendelian inheritance, achieving higher accuracy at lower coverage than single-individual methods.

Exploiting Next Generation Sequencing to solve the Haplotyping puzzle in Polyploids: a Simulation study

This study evaluates polyploid haplotyping methods using a simulation pipeline, finding that sequencing depth is key and all methods struggle with higher ploidy levels.