4.7 Article

Benchmarking small-variant genotyping in polyploids

Related references

Note: Only part of the references are listed.
Article Biology

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

Caroline Belser et al.

Summary: A chromosome-scale assembly of a banana genome (Musa acuminata) was reported using Oxford Nanopore long-reads, with five out of the eleven chromosomes entirely reconstructed in a single contig from telomere to telomere, revealing the content of complex regions like centromeres or clusters of paralogous genes for the first time.

COMMUNICATIONS BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

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

Daniel P. Cooke et al.

Summary: Octopus is a variant caller that uses a polymorphic Bayesian genotyping model capable of modeling different experimental designs within a unified haplotype-aware framework. It accurately calls germline variants in individuals, including low-frequency somatic variations, while producing fewer false positives compared to other methods. Octopus also outputs realigned evidence BAM files to assist with validation and interpretation.

NATURE BIOTECHNOLOGY (2021)

Article Biochemical Research Methods

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

Zhen Yao et al.

BMC BIOINFORMATICS (2020)

Article Biotechnology & Applied Microbiology

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

Peter Krusche et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

An open resource for accurately benchmarking small variant and reference calls

Justin M. Zook et al.

NATURE BIOTECHNOLOGY (2019)

Review Biotechnology & Applied Microbiology

Breeding crops to feed 10 billion

Lee T. Hickey et al.

NATURE BIOTECHNOLOGY (2019)

Article Genetics & Heredity

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

Lindsay V. Clark et al.

G3-GENES GENOMES GENETICS (2019)

Correction Biochemical Research Methods

Snakemake-a scalable bioinformatics workflow engine (vol 28, pg 2520, 2012)

Johannes Koster et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Strelka2: fast and accurate calling of germline and somatic variants

Sangtae Kim et al.

NATURE METHODS (2018)

Article Biochemical Research Methods

A synthetic-diploid benchmark for accurate variant-calling evaluation

Heng Li et al.

NATURE METHODS (2018)

Review Plant Sciences

Tools for Genetic Studies in Experimental Populations of Polyploids

Peter M. Bourke et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Biotechnology & Applied Microbiology

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

Ryan Poplin et al.

NATURE BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

The transcriptional landscape of polyploid wheat

R. H. Ramirez-Gonzalez et al.

SCIENCE (2018)

Article Genetics & Heredity

Genome amplification and cellular senescence are hallmarks of human placenta development

Philipp Velicky et al.

PLOS GENETICS (2018)

Review Plant Sciences

Current Strategies of Polyploid Plant Genome Sequence Assembly

Maria Kyriakidou et al.

FRONTIERS IN PLANT SCIENCE (2018)

Article Genetics & Heredity

Genotyping Polyploids from Messy Sequencing Data

David Gerard et al.

GENETICS (2018)

Article Biochemical Research Methods

SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Paul D. Blischak et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R. Conway et al.

BIOINFORMATICS (2017)

Review Biochemistry & Molecular Biology

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

Changsoo Kim et al.

PLANT SCIENCE (2016)

Review Biochemistry & Molecular Biology

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

Josh Clevenger et al.

MOLECULAR PLANT (2015)

Article Multidisciplinary Sciences

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

Jan G. A. M. L. Uitdewilligen et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

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

Angelique D'Hont et al.

NATURE (2012)

Review Biology

Polyploid organisms

Song Can et al.

SCIENCE CHINA-LIFE SCIENCES (2012)

Article Multidisciplinary Sciences

Genome sequence and analysis of the tuber crop potato

Xun Xu et al.

NATURE (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)