The complete sequence of a human Y chromosome

Jasmine and Iris: population-scale structural variant comparison and analysis

(2023) Melanie Kirsche et al.   NATURE METHODS

A draft human pangenome reference

(2023) Wen-Wei Liao et al.   NATURE

Telomere-to-telomere assembly of diploid chromosomes with Verkko

(2023) Mikko Rautiainen et al.   NATURE BIOTECHNOLOGY

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

(2023) Matthias H. Weissensteiner et al.   GENOME RESEARCH

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

(2023) Pille Hallast et al.   NATURE

Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

(2023) Chen-Shan Chin et al.   NATURE METHODS

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

(2022) Mitchell R Vollger et al.   BIOINFORMATICS

Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

(2022) David Porubsky et al.   CELL

Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment

(2022) Bill Tseng et al.   JOURNAL OF HUMAN GENETICS

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation

(2022) Giulio Formenti et al.   NATURE METHODS

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

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

Long-read mapping to repetitive reference sequences using Winnowmap2

(2022) Chirag Jain 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

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

(2022) Savannah J. Hoyt et al.   SCIENCE

A complete reference genome improves analysis of human genetic variation

(2022) Sergey Aganezov et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Segmental duplications and their variation in a complete human genome

(2022) Mitchell R. Vollger et al.   SCIENCE

A classical revival: Human satellite DNAs enter the genomics era

(2022) Nicolas Altemose   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families

(2022) Brianna Chrisman et al.   Scientific Reports

A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes

(2022) Reza Halabian et al.   Biology-Basel

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

(2022) Marta Byrska-Bishop et al.   CELL

Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch)

(2022) Merly Escalona et al.   JOURNAL OF HEREDITY

Semi-automated assembly of high-quality diploid human reference genomes

(2022) Erich D. Jarvis et al.   NATURE

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

(2022) Andrey V. Bzikadze et al.   GENOME RESEARCH

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over

(2021) Andrea Talenti et al.   Genome Biology and Evolution

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

(2021) Kishwar Shafin et al.   NATURE METHODS

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

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

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity

(2020) Marina Svetec Miklenić et al.   DNA REPAIR

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

(2020) Karen H. Miga et al.   NATURE

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

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Identifying centromeric satellites with dna-brnn

(2019) Heng Li   BIOINFORMATICS

Human contamination in bacterial genomes has created thousands of spurious proteins

(2019) Florian P. Breitwieser et al.   GENOME RESEARCH

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data

(2019) Timothy H Webster et al.   GigaScience

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data

(2019) David Porubsky et al.   BIOINFORMATICS

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

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

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes

(2019) Rahulsimham Vegesna et al.   PLoS Genetics

Kalign 3: multiple sequence alignment of large datasets

(2019) Timo Lassmann   BIOINFORMATICS

ClinVar: improvements to accessing data

(2019) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

(2019) Ashley D. Sanders et al.   NATURE BIOTECHNOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

(2018) Amanda L. Pendleton et al.   BMC BIOLOGY

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

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

Non-B-Form DNA Is Enriched at Centromeres

(2018) Sivakanthan Kasinathan 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

Accurate detection of complex structural variations using single-molecule sequencing

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

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages

(2018) Levi S. Teitz et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello 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

Short inverted repeats contribute to localized mutability in human somatic cells

(2017) Xueqing Zou et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Machine learning model for sequence-driven DNA G-quadruplex formation

(2017) Aleksandr B. Sahakyan et al.   Scientific Reports

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

(2016) Swapan Mallick et al.   NATURE

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

(2016) G David Poznik et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

(2016) Zachary D. Stephens et al.   PLoS One

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Centromere reference models for human chromosomes X and Y satellite arrays

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

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

(2014) Nicolas Altemose et al.   PLoS Computational Biology

nhmmer: DNA homology search with profile HMMs

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

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

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

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

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

(2013) G. D. Poznik et al.   SCIENCE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Ester Falconer et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes

(2011) Yali Xue et al.   Genes

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Copy number variation on the human Y chromosome

(2009) M.A. Jobling   CYTOGENETIC AND GENOME RESEARCH

Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood

(2009) Michael F. Hammer et al.   HUMAN GENETICS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

Splign: algorithms for computing spliced alignments with identification of paralogs

(2008) Yuri Kapustin et al.   Biology Direct

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

DupMasker: A tool for annotating primate segmental duplications

(2008) Z. Jiang et al.   GENOME RESEARCH