The complete sequence of a human genome

Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence

(2022) Christopher A. Miller et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

(2022) Ann M. Mc Cartney et al.   NATURE METHODS

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

Epigenetic patterns in a complete human genome

(2022) Ariel Gershman et al.   SCIENCE

A complete reference genome improves analysis of human genetic variation

(2022) Sergey Aganezov et al.   SCIENCE

Segmental duplications and their variation in a complete human genome

(2022) Mitchell R. Vollger et al.   SCIENCE

MBG: Minimizer-based Sparse de Bruijn Graph Construction

(2021) Mikko Rautiainen et al.   BIOINFORMATICS

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

The Need for a Human Pangenome Reference Sequence

(2021) Karen H. Miga et al.   Annual Review of Genomics and Human Genetics

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

(2021) Kishwar Shafin et al.   NATURE METHODS

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals

(2020) Lu Chen et al.   CELL

Evolutionary dynamics of abundant 7 bp satellites in the genome of Drosophila virilis

(2020) Jullien M Flynn et al.   MOLECULAR BIOLOGY AND EVOLUTION

GenMap: ultra-fast computation of genome mappability

(2020) Christopher Pockrandt et al.   BIOINFORMATICS

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

(2020) Alla Mikheenko et al.   BIOINFORMATICS

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

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

(2020) Karen H. Miga et al.   NATURE

Automated assembly of centromeres from ultra-long error-prone reads

(2020) Andrey V. Bzikadze et al.   NATURE BIOTECHNOLOGY

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads

(2019) Mitchell R. Vollger et al.   ANNALS OF HUMAN GENETICS

Human NORs, comprising rDNA arrays and functionally conserved distal elements, are located within dynamic chromosomal regions

(2019) Marjolein van Sluis et al.   GENES & DEVELOPMENT

Mechanisms of rDNA Copy Number Maintenance

(2019) Jonathan O. Nelson et al.   TRENDS IN GENETICS

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization

(2018) Maryam Ghareghani et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

(2018) Ian T. Fiddes et al.   GENOME RESEARCH

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

(2018) Jung-Hyun Kim et al.   NUCLEIC ACIDS RESEARCH

Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis

(2018) Mikael S. Lindström et al.   ONCOGENE

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias

(2018) Raga Krishnakumar et al.   Scientific Reports

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

(2018) Matthew M. Parks et al.   Science Advances

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

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

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

(2018) Wilfried M. Guiblet et al.   GENOME RESEARCH

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Long-read sequence and assembly of segmental duplications

(2018) Mitchell R. Vollger et al.   NATURE METHODS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

(2017) Ashley D Sanders et al.   Nature Protocols

A high-coverage Neandertal genome from Vindija Cave in Croatia

(2017) Kay Prüfer et al.   SCIENCE

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Mouse models of Down syndrome: gene content and consequences

(2016) Meenal Gupta et al.   MAMMALIAN GENOME

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Single haplotype assembly of the human genome from a hydatidiform mole

(2014) Karyn Meltz Steinberg et al.   GENOME RESEARCH

Centromere reference models for human chromosomes X and Y satellite arrays

(2014) K. H. Miga et al.   GENOME RESEARCH

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Heterochromatin variants in human karyotypes: a possible association with reproductive failure

(2014) Antonín Šípek et al.   REPRODUCTIVE BIOMEDICINE ONLINE

RFMix: A Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference

(2013) Brian K. Maples et al.   AMERICAN JOURNAL OF HUMAN GENETICS

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

The shared genomic architecture of human nucleolar organizer regions

(2013) I. Floutsakou et al.   GENOME RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution

(2012) Ester Falconer et al.   NATURE METHODS

Genomic size of CENP-A domain is proportional to total alpha satellite array size at human centromeres and expands in cancer cells

(2011) Lori L. Sullivan et al.   CHROMOSOME RESEARCH

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy

(2010) R. J. L. F. Lemmers et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Histone Modifications within the Human X Centromere Region

(2009) Brankica Mravinac et al.   PLoS One

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY