Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions

A critical comparison of technologies for a plant genome sequencing project

(2019) Pirita Paajanen et al.   GigaScience

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

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

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

(2017) Lasse Maretty et al.   NATURE

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

(2017) Ruibang Luo et al.   Computational and Structural Biotechnology Journal

LongISLND:in silicosequencing of lengthy and noisy datatypes

(2016) Bayo Lau et al.   BIOINFORMATICS

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

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

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

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

Biased Allelic Expression in Human Primary Fibroblast Single Cells

(2015) Christelle Borel et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

De novo assembly of a haplotype-resolved human genome

(2015) Hongzhi Cao et al.   NATURE BIOTECHNOLOGY

A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly

(2015) Hideki Nishikawa et al.   NATURE GENETICS

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

(2015) Sangeet Lamichhaney et al.   NATURE GENETICS

A supergene determines highly divergent male reproductive morphs in the ruff

(2015) Clemens Küpper et al.   NATURE GENETICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

(2015) M. Malinsky et al.   SCIENCE

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

(2014) Shengfeng Huang et al.   Nature Communications

Major Histocompatibility Complex Genomics and Human Disease

(2013) John Trowsdale et al.   Annual Review of Genomics and Human Genetics

Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes

(2013) Heini M. Natri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Structure and evolution of the sea star egg receptor for sperm bindin

(2013) Michael W. Hart   MOLECULAR ECOLOGY

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity

(2012) G. Zhang et al.   SCIENCE

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE