Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Telomere-to-telomere assembly of diploid chromosomes with Verkko

(2023) Mikko Rautiainen et al.   NATURE BIOTECHNOLOGY

The complete sequence of a human Y chromosome

(2023) Arang Rhie et al.   NATURE

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

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

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

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

(2022) Marta Byrska-Bishop et al.   CELL

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

(2021) Jessica Storer et al.   Mobile DNA

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

(2021) Haoyu Cheng et al.   NATURE METHODS

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

Origin and diffusion of human Y chromosome haplogroup J1-M267

(2021) Hovhannes Sahakyan et al.   Scientific Reports

lra: A long read aligner for sequences and contigs

(2021) Jingwen Ren et al.   PLoS Computational Biology

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

(2021) Kishwar Shafin et al.   NATURE METHODS

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

The Drosophila Y chromosome affects heterochromatin integrity genome-wide

(2020) Emily J Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) Alla Mikheenko et al.   BIOINFORMATICS

A Southeast Asian origin for present-day non-African human Y chromosomes

(2020) Pille Hallast et al.   HUMAN GENETICS

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

(2020) Karen H. Miga et al.   NATURE

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

(2020) David Heller et al.   BIOINFORMATICS

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

(2020) Dandan Lang et al.   GigaScience

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

(2019) Liang Gong et al.   Jove-Journal of Visualized Experiments

Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome

(2019) Wentao Shi et al.   HUMAN MOLECULAR GENETICS

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

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

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

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

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

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

(2019) Weichen Zhou et al.   NUCLEIC ACIDS RESEARCH

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

Long-read sequence and assembly of segmental duplications

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

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

(2018) Lukas F. K. Kuderna et al.   Nature Communications

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

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

(2017) Ashley D Sanders et al.   Nature Protocols

Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion

(2017) Laurits Skov et al.   PLoS Genetics

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

(2016) G David Poznik et al.   NATURE GENETICS

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

(2015) Monika Karmin et al.   GENOME RESEARCH

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The Y-chromosome point mutation rate in humans

(2015) Agnar Helgason et al.   NATURE GENETICS

Efficient set tests for the genetic analysis of correlated traits

(2015) Francesco Paolo Casale et al.   NATURE METHODS

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

DYZ1 arrays show sequence variation between the monozygotic males

(2014) Sandeep Yadav et al.   BMC GENETICS

Centromere reference models for human chromosomes X and Y satellite arrays

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of a 45,000-year-old modern human from western Siberia

(2014) Qiaomei Fu et al.   NATURE

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

(2014) Nicolas Altemose et al.   PLoS Computational Biology

Natural Selection Reduced Diversity on Human Y Chromosomes

(2014) Melissa A. Wilson Sayres et al.   PLoS Genetics

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

(2013) Fernando L. Mendez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao 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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

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

(2012) Ester Falconer et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

(2011) Yali Xue et al.   Genes

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes

(2009) Julian Lange et al.   CELL