Assembly of complete diploid-phased chromosomes from draft genome sequences

Diploid chromosome-scale assembly of the Muscadinia rotundifolia genome supports chromosome fusion and disease resistance gene expansion during Vitis and Muscadinia divergence

(2021) Noé Cochetel et al.   G3-Genes Genomes Genetics

Rootstock influences the effect of grapevine leafroll‐associated viruses on berry development and metabolism via abscisic acid signalling

(2021) Amanda M. Vondras et al.   MOLECULAR PLANT PATHOLOGY

Large structural variations in the haplotype‐resolved African cassava genome

(2021) Ben N. Mansfeld et al.   PLANT JOURNAL

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

(2020) Cheng Zou et al.   Nature Communications

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

(2020) Peng Zhou et al.   PLANT CELL

Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle

(2020) Wai Yee Low et al.   Nature Communications

De novo assembly of the cattle reference genome with single-molecule sequencing

(2020) Benjamin D Rosen et al.   GigaScience

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

The genetic basis of sex determination in grapes

(2020) Mélanie Massonnet et al.   Nature Communications

Chromosome-scale, haplotype-resolved assembly of human genomes

(2020) Shilpa Garg et al.   NATURE BIOTECHNOLOGY

A critical comparison of technologies for a plant genome sequencing project

(2019) Pirita Paajanen et al.   GigaScience

Diploid Genome Assembly of the Wine Grape Carménère

(2019) Andrea Minio et al.   G3-Genes Genomes Genetics

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

(2019) Andreas Wallberg et al.   BMC GENOMICS

The Whole-Genome Sequence of the Coral Acropora millepora

(2019) Hua Ying et al.   Genome Biology and Evolution

Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees

(2019) Jennafer A. P. Hamlin et al.   G3-Genes Genomes Genetics

Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

(2019) Huilong Du et al.   Nature Communications

A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution

(2019) Lorenzo Barchi et al.   Scientific Reports

The genomic diversification of grapevine clones

(2019) Amanda M. Vondras et al.   BMC GENOMICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

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

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

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

(2016) Gaik Tamazian et al.   GigaScience

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Whole genome comparison between table and wine grapes reveals a comprehensive catalog of structural variants

(2014) Alex Di Genova et al.   BMC PLANT BIOLOGY

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

(2013) H. Hirakawa et al.   DNA RESEARCH

Reference-assisted chromosome assembly

(2013) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

(2012) Yi Ren et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS