CoChat
Sign Up
Cited by 471Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

The complete sequence of a human Y chromosome

Open access
Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J., Taylor, Dylan J., Altemose, Nicolas, Hook, Paul W., Koren, Sergey +79 more·2023·Nature
DOI 10.1038/s41586-023-06457-yPMC PMC10752217

Published version of a preprint

Open this paper in CoChat — free accountOpen PDF

Abstract

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications 1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished 4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome 4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41586-023-06457-y

Cites

24 of 24 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Tools like Cactus and Progressive Cactus utilize a combination of heuristic and exact methods to generate accurate alignments quickly.

    “For instance, tools like Cactus and Progressive Cactus utilize a combination of heuristic and exact methods to generate accurate alignments quickly [62].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [62]

    The References (no page provided) identify Progressive Cactus as a multiple-genome aligner, supporting its identification as an alignment tool. The paper does not describe Cactus or Progressive Cactus combining heuristic and exact methods, or establish the claimed speed and accuracy. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Newer tools like Cactus and Progressive Cactus have incorporated mechanisms to accurately align regions with inversions, duplications, and translocations.

    “While traditional alignment algorithms often struggle with these rearrangements, newer tools like Cactus and Progressive Cactus have incorporated mechanisms to accurately align regions with inversions, duplications, and translocations [62].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [62]

    The References list Progressive Cactus as a multiple-genome aligner, but do not describe its mechanisms or performance on inversions, duplications, or translocations. The Online Methods describe other alignment tools; searches for Cactus and alignment of those rearrangements found no passage addressing the attributed claim. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 123

  1. [1]Skaletsky H The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825– 837 (2003). 12815422
  2. [2]Miga KH Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697– 707 (2014). 24501022 PMC3975068
  3. [4]Nurk S The complete sequence of a human genome. Science 376, 44– 53 (2022). 35357919 PMC9186530
  4. [6]Gustafson ML, M. D. & Donahoe PK, M. D. MALE SEX DETERMINATION: Current Concepts of Male Sexual Differentiation. Annu. Rev. Med 45, 505– 524 (1994). 8198399
  5. [7]Vog PH Human Y Chromosome Azoospermia Factors (AZF) Mapped to Different Subregions in Yq11. Hum. Mol. Genet 5, 933– 943 (1996). 8817327
  6. [8]Miga KH Telomere-to-telomere assembly of a complete human X chromosome. Nature 585, 79– 84 (2020). 32663838 PMC7484160
  7. [9]Logsdon GA The structure, function and evolution of a complete human chromosome 8. Nature 593, 101– 107 (2021). 33828295 PMC8099727
  8. [11]Jain M Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol 36, 338– 345 (2018). 29431738 PMC5889714
  9. [12]Nurk S HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res. gr 263566.120 (2020) doi: 10.1101/gr.263566.120. PMC7545148 32801147 · DOI
  10. [13]Rautiainen M & Marschall T GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol. 21, 253 (2020). 32972461 PMC7513500
  11. [14]Formenti G Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. Nat. Methods 19, 696– 704 (2022). 35361932 PMC9745813
  12. [15]Kirsche M Jasmine and Iris: population-scale structural variant comparison and analysis. Nat. Methods 20, 408– 417 (2023). 36658279 PMC10006329
  13. [16]Jain C, Rhie A, Hansen NF, Koren S & Phillippy AM Long-read mapping to repetitive reference sequences using Winnowmap2. Nat. Methods 19, 705– 710 (2022). 35365778 PMC10510034
  14. [17]Mc Cartney AM Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat. Methods 19, 687– 695 (2022). 35361931 PMC9812399
  15. [18]Rhie A, Walenz BP, Koren S & Phillippy AM Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020). 32928274 PMC7488777
  16. [19]Wang T The Human Pangenome Project: a global resource to map genomic diversity. Nature 604, 437– 446 (2022). 35444317 PMC9402379
  17. [21]Shumate A Assembly and annotation of an Ashkenazi human reference genome. Genome Biol. 21, 129 (2020). 32487205 PMC7265644
  18. [23]Landrum MJ ClinVar: improvements to accessing data. Nucleic Acids Res. 48, D835– D844 (2020). 31777943 PMC6943040
  19. [24]Welter D The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001– D1006 (2014). 24316577 PMC3965119
  20. [25]Smigielski EM, Sirotkin K, Ward M & Sherry ST dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res. 28, 352– 355 (2000). 10592272 PMC102496
  21. [26]Karczewski KJ The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434– 443 (2020). 32461654 PMC7334197
  22. [27]Byrska-Bishop M High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 185, 3426– 3440.e19 (2022). 36055201 PMC9439720
  23. [29]Dunham I An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57– 74 (2012). 22955616 PMC3439153
  24. [31]Sanders AD Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat. Biotechnol 38, 343– 354 (2020). 31873213 PMC7612647
  25. [32]Hallast Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation. Nature (2023). In press, doi: 10.1038/s41586-023-06425-6 PMC10726138 37612510 · DOI
  26. [33]Hammer MF Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood. Hum. Genet 126, 707 (2009). 19669163 PMC2771134
  27. [34]Poznik GD Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat. Genet 48, 593– 599 (2016). 27111036 PMC4884158
  28. [35]Jiang Z, Hubley R, Smit A & Eichler EE DupMasker: a tool for annotating primate segmental duplications. Genome Res. 18, 1362– 1368 (2008). 18502942 PMC2493431
  29. [36]Vollger MR, Kerpedjiev P, Phillippy AM & Eichler EE StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. Bioinformatics 38, 2049– 2051 (2022). 35020798 PMC8963321
  30. [37]Vegesna R, Tomaszkiewicz M, Medvedev P & Makova KD Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PLOS Genet. 15, e1008369 (2019). 31525193 PMC6772104
  31. [40]Warburton PE Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 9, 533 (2008). 18992157 PMC2588610
  32. [41]Halabian R & Makałowski W A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes. Biology 11, 1032 (2022). 36101413 PMC9311842
  33. [42]Weissensteiner MH Accurate sequencing of DNA motifs able to form alternative (non-B) structures. Genome Res. 33, 907– 922 (2023). 37433640 PMC10519405
  34. [43]Tyler-Smith C, Taylor L & Müller U Structure of a hypervariable tandemly repeated DNA sequence on the short arm of the human Y chromosome. J. Mol. Biol 203, 837– 848 (1988). 3210241
  35. [44]Xue Y & Tyler-Smith C An Exceptional Gene: Evolution of the TSPY Gene Family in Humans and Other Great Apes. Genes 2, 36– 47 (2011). 24710137 PMC3924835
  36. [45]Saxena R Four DAZ Genes in Two Clusters Found in the AZFc Region of the Human Y Chromosome. Genomics 67, 256– 267 (2000). 10936047
  37. [46]Altemose N Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178 (2022). 35357911 PMC9233505
  38. [47]Jain M Linear assembly of a human centromere on the Y chromosome. Nat. Biotechnol 36, 321– 323 (2018). 29553574 PMC5886786
  39. [49]Kasinathan S & Henikoff S Non-B-Form DNA Is Enriched at Centromeres. Mol. Biol. Evol 35, 949– 962 (2018). 29365169 PMC5889037
  40. [50]Skene PJ & Henikoff S An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017). 28079019 PMC5310842
  41. [51]Nailwal M & Chauhan JB Azoospermia factor C subregion of the Y chromosome. J. Hum. Reprod. Sci 10, 256 (2017). 29430151 PMC5799928
  42. [52]Kuroda-Kawaguchi T The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men. Nat. Genet 29, 279– 286 (2001). 11687796
  43. [53]Repping S A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region. Genomics 83, 1046– 1052 (2004). 15177557
  44. [54]Porubsky D Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986– 2005.e26 (2022). 35525246 PMC9563103
  45. [55]Teitz LS, Pyntikova T, Skaletsky H & Page DC Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am. J. Hum. Genet 103, 261– 275 (2018). 30075113 PMC6080837
  46. [56]Jobling MA Copy number variation on the human Y chromosome. Cytogenet. Genome Res 123, 253– 262 (2008). 19287162
  47. [57]Navarro-Costa P, Plancha CE & Gonçalves J Genetic Dissection of the AZF Regions of the Human Y Chromosome: Thriller or Filler for Male (In)fertility? BioMed Res. Int 2010, e936569 (2010). PMC2910558 20671934
  48. [59]Schmid M, Guttenbach M, Nanda I, Studer R & Epplen JT Organization of DYZ2 repetitive DNA on the human Y chromosome. Genomics 6, 212– 218 (1990). 2307465
  49. [60]Manz E, Alkan M, Bühler E & Schmidtke J Arrangement of DYZ1 and DYZ2 repeats on the human Y-chromosome: a case with presence of DYZ1 and absence of DYZ2. Mol. Cell. Probes 6, 257– 259 (1992). 1406735
  50. [61]Altemose N A classical revival: Human satellite DNAs enter the genomics era. Semin. Cell Dev. Biol 128, 2– 14 (2022). 35487859
  51. [62]Gripenberg U Size variation and orientation of the human Y chromosome. Chromosoma 15, 618– 629 (1964). 14333154
  52. [63]Mathias N, Bayés M & Tyler-Smith C Highly informative compound haplotypes for the human Y chromosome. Hum. Mol. Genet 3, 115– 123 (1994). 7909247
  53. [64]Altemose N, Miga KH, Maggioni M & Willard HF Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly. PLOS Comput. Biol 10, e1003628 (2014). 24831296 PMC4022460
  54. [65]Cooke H Repeated sequence specific to human males. Nature 262, 182– 186 (1976). 819844
  55. [66]Frommer M, Prosser J & Vincent PC Human satellite I sequences include a male specific 2.47 kb tandemly repeated unit containing one Alu family member per repeat. Nucleic Acids Res. 12, 2887– 2900 (1984). 6324132 PMC318713
  56. [67]Babcock M, Yatsenko S, Stankiewicz P, Lupski JR & Morrow BE AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. Genome Res. 17, 451– 460 (2007). 17284672 PMC1832092
  57. [68]Webster TH Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data. GigaScience 8, giz074 (2019). 31289836 PMC6615978
  58. [69]Aganezov S A complete reference genome improves analysis of human genetic variation. Science 376, eabl3533 (2022). 35357935 PMC9336181
  59. [71]Robinson JT Integrative genomics viewer. Nat. Biotechnol 29, 24– 26 (2011). 21221095 PMC3346182
  60. [72]Breitwieser FP, Pertea M, Zimin AV & Salzberg SL Human contamination in bacterial genomes has created thousands of spurious proteins. Genome Res. 29, 954– 960 (2019). 31064768 PMC6581058
  61. [74]Chrisman B The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families. Sci. Rep 12, 9863 (2022). 35701436 PMC9198055
  62. [75]Kent WJ The Human Genome Browser at UCSC. Genome Res. 12, 996– 1006 (2002). 12045153 PMC186604
  63. [76]Rautiainen M Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat. Biotechnol 1–9 (2023) doi: 10.1038/s41587-023-01662-6. PMC10427740 36797493 · DOI
  64. [79]Koren S De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol 36, 1174– 1182 (2018). PMC6476705 30346939
  65. [80]Kolmogorov M, Yuan J, Lin Y & Pevzner PA Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol 37, 540– 546 (2019). 30936562
  66. [82]Shafin K Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat. Methods 18, 1322– 1332 (2021). 34725481 PMC8571015
  67. [83]Sedlazeck FJ Accurate detection of complex structural variations using single molecule sequencing. Nat. Methods 15, 461– 468 (2018). 29713083 PMC5990442
  68. [84]Jiang T Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 21, 189 (2020). 32746918 PMC7477834
  69. [85]Bzikadze AV, Mikheenko A & Pevzner PA Fast and accurate mapping of long reads to complete genome assemblies with VerityMap. Genome Res. gr 276871.122 (2022) doi: 10.1101/gr.276871.122. PMC9808623 36379716 · DOI
  70. [87]Porubsky D breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics 36, 1260– 1261 (2020). 31504176
  71. [90]Tseng B Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J. Hum. Genet 67, 487– 493 (2022). 35347230
  72. [91]Li H Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094– 3100 (2018). 29750242 PMC6137996
  73. [94]Morgulis A, Gertz EM, Schäffer AA & Agarwala R WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22, 134– 141 (2006). 16287941
  74. [95]Chin C-S Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat. Methods 1– 9 (2023) doi: 10.1038/s41592-023-01914-y. 37365340 PMC10406601 · DOI
  75. [96]Frankish A GENCODE 2021. Nucleic Acids Res. 49, D916– D923 (2021). 33270111 PMC7778937
  76. [98]Kovaka S Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol. 20, 278 (2019). 31842956 PMC6912988
  77. [99]Stanke M, Diekhans M, Baertsch R & Haussler D Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637– 644 (2008). 18218656
  78. [100]Fiddes IT Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation. Genome Res. 28, 1029– 1038 (2018). 29884752 PMC6028123
  79. [101]Shumate A & Salzberg SL Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639– 1643 (2021). 33320174 PMC8289374
  80. [102]Dale RK, Pedersen BS & Quinlan AR Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27, 3423– 3424 (2011). 21949271 PMC3232365
  81. [103]Rhie A Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737– 746 (2021). 33911273 PMC8081667
  82. [104]Pruitt KD RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42, D756– 763 (2014). 24259432 PMC3965018
  83. [105]Kapustin Y, Souvorov A, Tatusova T & Lipman D Splign: algorithms for computing spliced alignments with identification of paralogs. Biol. Direct 3, 20 (2008). 18495041 PMC2440734
  84. [106]Katoh K & Standley DM MAFFT: Iterative Refinement and Additional Methods. in Multiple Sequence Alignment Methods (ed. Russell DJ) 131– 146 (Humana Press, 2014). doi: 10.1007/978-1-62703-646-7_8. 24170399 · DOI
  85. [107]Slater GSC & Birney E Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31 (2005). 15713233 PMC553969
  86. [108]Zook JM Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol 32, 246– 251 (2014). 24531798
  87. [109]Numanagić I Fast characterization of segmental duplications in genome assemblies. Bioinformatics 34, i706– i714 (2018). 30423092 PMC6129265
  88. [112]Storer J, Hubley R, Rosen J, Wheeler TJ & Smit AF The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob. DNA 12, 2 (2021). 33436076 PMC7805219
  89. [113]Olson D & Wheeler T ULTRA: a model based tool to detect tandem repeats. ACM BCB 2018, 37– 46 (2018). 31080962 PMC6508075
  90. [115]Storer JM, Hubley R, Rosen J & Smit AF A. Curation Guidelines for de novo Generated Transposable Element Families. Curr. Protoc 1, e154 (2021). 34138525 PMC9191830
  91. [116]Kent WJ BLAT—The BLAST-Like Alignment Tool. Genome Res. 12, 656– 664 (2002). 11932250 PMC187518
  92. [118]Altschul SF, Gish W, Miller W, Myers EW & Lipman DJ Basic local alignment search tool. J. Mol. Biol 215, 403– 410 (1990). 2231712
  93. [119]Cer R. z. Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool). Curr. Protoc. Hum. Genet 73, 18.7.1– 18.7.22 (2012). PMC3350812 22470144
  94. [120]Zou X Short inverted repeats contribute to localized mutability in human somatic cells. Nucleic Acids Res. 45, 11213– 11221 (2017). 28977645 PMC5737083
  95. [121]Svetec Miklenić M Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair 90, 102848 (2020). 32388488
  96. [122]Sahakyan AB Machine learning model for sequence-driven DNA G-quadruplex formation. Sci. Rep 7, 14535 (2017). 29109402 PMC5673958
  97. [123]Hao Z RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput. Sci 6, e251 (2020). PMC7924719 33816903
  98. [127]Hach F mrsFAST: a cache-oblivious algorithm for short-read mapping. Nat. Methods 7, 576– 577 (2010). 20676076 PMC3115707
  99. [128]Escalona M Whole-genome sequence and assembly of the Javan gibbon (Hylobates moloch). J. Hered 114, 35– 43 (2023). 36146896 PMC10019027
  100. [129]Cortez D Origins and functional evolution of Y chromosomes across mammals. Nature 508, 488– 493 (2014). 24759410
  101. [130]Stamatakis A RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312– 1313 (2014). 24451623 PMC3998144
  102. [133]Tyler-Smith C & Brown WRA Structure of the major block of alphoid satellite DNA on the human Y chromosome. J. Mol. Biol 195, 457– 470 (1987). 2821279
  103. [134]Shepelev VA Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly. Genomics Data 5, 139– 146 (2015). 26167452 PMC4496801
  104. [135]Lee I Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat. Methods 17, 1191– 1199 (2020). 33230324 PMC7704922
  105. [136]Krumsiek J, Arnold R & Rattei T Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23, 1026– 1028 (2007). 17309896
  106. [137]Rice P, Longden I & Bleasby A EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276– 277 (2000). 10827456
  107. [139]Lassmann T Kalign 3: multiple sequence alignment of large datasets. Bioinformatics 36, 1928– 1929 (2020). PMC7703769 31665271
  108. [140]Wheeler TJ & Eddy SR nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487– 2489 (2013). 23842809 PMC3777106
  109. [141]Stephens ZD Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models. PLOS ONE 11, e0167047 (2016). 27893777 PMC5125660
  110. [142]Bushnell B BBMap: A Fast, Accurate, Splice-Aware Aligner. https://www.osti.gov/biblio/1241166 (2014).
  111. [144]Poznik GD Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science 341, 562– 565 (2013). 23908239 PMC4032117
  112. [145]McKenna A The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297– 1303 (2010). 20644199 PMC2928508
  113. [146]Schatz MC Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genomics 2, 100085 (2022). 35199087 PMC8863334
  114. [147]Danecek P Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021). 33590861 PMC7931819
  115. [148]Talenti A & Prendergast J nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. Genome Biol. Evol 13, evab183 (2021). 34383887 PMC8412297
  116. [150]Sherry ST, Ward M & Sirotkin K dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation. Genome Res. 9, 677– 679 (1999). 10447503
  117. [152]Buniello A The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47, D1005– D1012 (2019). 30445434 PMC6323933
  118. [154]Langmead B & Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357– 359 (2012). 22388286 PMC3322381
  119. [155]Ramírez F deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160– W165 (2016). 27079975 PMC4987876
  120. [156]Zhao H CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 1006– 1007 (2014). 24351709 PMC3967108
  121. [157]Marçais G MUMmer4: A fast and versatile genome alignment system. PLOS Comput. Biol 14, e1005944 (2018). 29373581 PMC5802927
  122. [158]Ondov BD, Bergman NH & Phillippy AM Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12, 385 (2011). 21961884 PMC3190407
  123. [159]Falconer E DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat. Methods 9, 1107– 1112 (2012). 23042453 PMC3580294

Cited by

Sorted by citations

Authors
Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., Allen, J., Asri, M., Bzikadze, A. V., Chen, N.-C., Chin, C.-S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., Garcia Giron, C., Garrison, E., Gershman, A., Gerton, J. L., Grady, P. G. S., Guarracino, A., Haggerty, L., Halabian, R., Hansen, N. F., Harris, R., Hartley, G. A., Harvey, W. T., Haukness, M., Heinz, J., Hourlier, T., Hubley, R. M., Hunt, S. E., Hwang, S., Jain, M., Kesharwani, R. K., Lewis, A. P., Li, H., Logsdon, G. A., Lucas, J. K., Makalowski, W., Markovic, C., Martin, F. J., Mc Cartney, A. M., McCoy, R. C., McDaniel, J., McNulty, B. M., Medvedev, P., Mikheenko, A., Munson, K. M., Murphy, T. D., Olsen, H. E., Olson, N. D., Paulin, L. F., Porubsky, D., Potapova, T., Ryabov, F., Salzberg, S. L., Sauria, M. E. G., Sedlazeck, F. J., Shafin, K., Shepelev, V. A., Shumate, A., Storer, J. M., Surapaneni, L., Taravella Oill, A. M., Thibaud-Nissen, F., Timp, W., Tomaszkiewicz, M., Vollger, M. R., Walenz, B. P., Watwood, A. C., Weissensteiner, M. H., Wenger, A. M., Wilson, M. A., Zarate, S., Zhu, Y., Zook, J. M., Eichler, E. E., O’Neill, R. J., Schatz, M. C., Miga, K. H., Makova, K. D., & Phillippy, A. M.
Affiliations
  • National Institutes of Health (US)
  • University of Connecticut (US)
  • Johns Hopkins University (US)
  • University of California, Berkeley (US)
  • Russian Academy of Sciences (RU)
  • European Bioinformatics Institute (GB)
  • University of California, Santa Cruz (US)
  • University of California San Diego (US)
  • Rockefeller University (US)
  • DNAnexus (United States) (US)
  • University of Tennessee Health Science Center (US)
  • Stowers Institute for Medical Research (US)
  • University of Münster (DE)
  • Pennsylvania State University (US)
  • University of Washington (US)
  • Institute for Systems Biology (US)
  • Northeastern University (US)
  • Baylor College of Medicine (US)
  • Harvard University (US)
  • Washington University in St. Louis (US)
  • National Institute of Standards and Technology (US)
  • St Petersburg University (RU)
  • National Research University Higher School of Economics (RU)
  • Google (United States) (US)
  • Institute of Molecular Genetics (RU)
  • Pacific Biosciences (United States) (US)
  • Arizona State University (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Phillippy, Adam M.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2023-08-23
Volume
621
Issue
7978
Pages
344-354
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-023-06457-y
PMC
PMC10752217
OpenAlex
W4386113054
Cited by
471
References
24
Citations by year
2026: 134 · 2025: 139 · 2024: 156 · 2023: 41 · 2022: 1
FWCI
75.59
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, other-oa)
  • UCL Discovery (University College London) (submittedVersion, other-oa)
  • Digital Commons-TMC (Texas Medical Center) (submittedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • National Science Foundation (1627442, HG002385, HG010169)
  • Howard Hughes Medical Institute
  • University of Pennsylvania
  • Arizona State University
  • University of Connecticut
  • Stowers Institute for Medical Research
  • Achievement Rewards for College Scientists Foundation
  • Pennsylvania State University
  • European Molecular Biology Laboratory
  • Saint Petersburg State University (73023672, PURE73023672)
  • Ministry of Science and Higher Education of the Russian Federation
  • National Institutes of Health (Z99 HG999999, 1s10od028587-01, HG006620, HG007234)
  • National Institute of Standards and Technology (70NANB21H101)
  • National Institute on Drug Abuse (U01DA047638)
  • National Human Genome Research Institute (HG010169, HG010136, HG011758, HG002939, R21HG010548, HG009190, U01HG010971, U41HG006620, U41HG007234, R01HG009190, HG006620, R01HG011274, U01HG010961, U24HG010263, R01HG010040, R01HG002385, U24HG007234, U24HG006620, UM1HG010971, R01HG010169, ZIAHG200398, R01HG002939, U41HG010972, U24HG010136, U01HG011758)
  • National Cancer Institute (R21CA240199, U01CA253481, R01CA266339)
  • National Institute of General Medical Sciences (R01GM136684, R01GM130691, R01GM072264, R01GM123312, R35GM124827, K99GM147352, T32GM007454, R35GM133747, R00GM147352)
  • U.S. National Library of Medicine
  • Division of Biological Infrastructure
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
human Y chromosome, complete genome sequence, RBMY
MeSH terms
Deleted in Azoospermia 1 Protein, Base Sequence, DNA, Satellite, Multigene Family, Genetics, Population, Heterochromatin, Humans, Nuclear Proteins, Reference Standards, Genetic Variation, RNA-Binding Proteins, Telomere, Sequence Analysis, DNA, Cell Cycle Proteins, Tandem Repeat Sequences, Genomics, Chromosomes, Human, Y, Segmental Duplications, Genomic

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review