GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

(2018) Reuben W. Nowell et al.   PLOS BIOLOGY

Clonal genome evolution and rapid invasive spread of the marbled crayfish

(2018) Julian Gutekunst et al.   Nature Ecology & Evolution

Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species

(2018) Li He et al.   CHROMOSOMA

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change

(2017) Amir Szitenberg et al.   Genome Biology and Evolution

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome diversity of tuber-bearingSolanumuncovers complex evolutionary history and targets of domestication in the cultivated potato

(2017) Michael A. Hardigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Whole genome duplication in coast redwood (Sequoia sempervirens ) and its implications for explaining the rarity of polyploidy in conifers

(2016) Alison Dawn Scott et al.   NEW PHYTOLOGIST

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

(2016) Michael A. Hardigan et al.   PLANT CELL

Doubling down on genomes: Polyploidy and crop plants

(2014) Simon Renny-Byfield et al.   AMERICAN JOURNAL OF BOTANY

KmerStream: streaming algorithms for k -mer abundance estimation

(2014) Páll Melsted et al.   BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Allotetraploid and autotetraploid models of linkage analysis

(2013) F. Xu et al.   BRIEFINGS IN BIOINFORMATICS

T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks

(2012) A. Boc et al.   NUCLEIC ACIDS RESEARCH

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY