Benchmarking small-variant genotyping in polyploids

A unified haplotype-based method for accurate and comprehensive variant calling

(2021) Daniel P. Cooke et al.   NATURE BIOTECHNOLOGY

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

(2021) Caroline Belser et al.   Communications Biology

Evaluation of variant calling tools for large plant genome re-sequencing

(2020) Zhen Yao et al.   BMC BIOINFORMATICS

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

(2019) Lindsay V. Clark et al.   G3-Genes Genomes Genetics

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

Breeding crops to feed 10 billion

(2019) Lee T. Hickey et al.   NATURE BIOTECHNOLOGY

Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2

(2019) Mareike Busche et al.   G3-Genes Genomes Genetics

Snakemake—a scalable bioinformatics workflow engine

(2018) Johannes Köster et al.   BIOINFORMATICS

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Tools for Genetic Studies in Experimental Populations of Polyploids

(2018) Peter M. Bourke et al.   Frontiers in Plant Science

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Genome amplification and cellular senescence are hallmarks of human placenta development

(2018) Philipp Velicky et al.   PLoS Genetics

Current Strategies of Polyploid Plant Genome Sequence Assembly

(2018) Maria Kyriakidou et al.   Frontiers in Plant Science

Application of genotyping by sequencing technology to a variety of crop breeding programs

(2016) Changsoo Kim et al.   PLANT SCIENCE

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations

(2015) Josh Clevenger et al.   Molecular Plant

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

(2014) Jiangfeng He et al.   Frontiers in Plant Science

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

Polyploid organisms

(2012) Can Song et al.   Science China-Life Sciences

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Sequencing crop genomes: approaches and applications

(2011) Scott A. Jackson et al.   NEW PHYTOLOGIST

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS