PT  - JOURNAL ARTICLE
AU  - Arang Rhie
AU  - Sergey Nurk
AU  - Monika Cechova
AU  - Savannah J. Hoyt
AU  - Dylan J. Taylor
AU  - Nicolas Altemose
AU  - Paul W. Hook
AU  - Sergey Koren
AU  - Mikko Rautiainen
AU  - Ivan A. Alexandrov
AU  - Jamie Allen
AU  - Mobin Asri
AU  - Andrey V. Bzikadze
AU  - Nae-Chyun Chen
AU  - Chen-Shan Chin
AU  - Mark Diekhans
AU  - Paul Flicek
AU  - Giulio Formenti
AU  - Arkarachai Fungtammasan
AU  - Carlos Garcia Giron
AU  - Erik Garrison
AU  - Ariel Gershman
AU  - Jennifer Gerton
AU  - Patrick G.S. Grady
AU  - Andrea Guarracino
AU  - Leanne Haggerty
AU  - Reza Halabian
AU  - Nancy F. Hansen
AU  - Robert Harris
AU  - Gabrielle A. Hartley
AU  - William T. Harvey
AU  - Marina Haukness
AU  - Jakob Heinz
AU  - Thibaut Hourlier
AU  - Robert M. Hubley
AU  - Sarah E. Hunt
AU  - Stephen Hwang
AU  - Miten Jain
AU  - Rupesh K. Kesharwani
AU  - Alexandra P. Lewis
AU  - Heng Li
AU  - Glennis A. Logsdon
AU  - Julian K. Lucas
AU  - Wojciech Makalowski
AU  - Christopher Markovic
AU  - Fergal J. Martin
AU  - Ann M. Mc Cartney
AU  - Rajiv C. McCoy
AU  - Jennifer McDaniel
AU  - Brandy M. McNulty
AU  - Paul Medvedev
AU  - Alla Mikheenko
AU  - Katherine M. Munson
AU  - Terence D. Murphy
AU  - Hugh E. Olsen
AU  - Nathan D. Olson
AU  - Luis F. Paulin
AU  - David Porubsky
AU  - Tamara Potapova
AU  - Fedor Ryabov
AU  - Steven L. Salzberg
AU  - Michael E.G. Sauria
AU  - Fritz J. Sedlazeck
AU  - Kishwar Shafin
AU  - Valery A. Shepelev
AU  - Alaina Shumate
AU  - Jessica M. Storer
AU  - Likhitha Surapaneni
AU  - Angela M. Taravella Oill
AU  - Françoise Thibaud-Nissen
AU  - Winston Timp
AU  - Marta Tomaszkiewicz
AU  - Mitchell R. Vollger
AU  - Brian P. Walenz
AU  - Allison C. Watwood
AU  - Matthias H. Weissensteiner
AU  - Aaron M. Wenger
AU  - Melissa A. Wilson
AU  - Samantha Zarate
AU  - Yiming Zhu
AU  - Justin M. Zook
AU  - Evan E. Eichler
AU  - Rachel O’Neill
AU  - Michael C. Schatz
AU  - Karen H. Miga
AU  - Kateryna D. Makova
AU  - Adam M. Phillippy
TI  - The complete sequence of a human Y chromosome
AID  - 10.1101/2022.12.01.518724
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.12.01.518724
4099  - http://biorxiv.org/content/early/2022/12/01/2022.12.01.518724.short
4100  - http://biorxiv.org/content/early/2022/12/01/2022.12.01.518724.full
AB  - The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications. 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. 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, revealing the complete ampliconic structures of TSPY, DAZ, and RBMY; 42 additional protein-coding genes, mostly from the TSPY gene family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a prior assembly of the CHM13 genome and mapped available population variation, clinical variants, and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.Competing Interest StatementS.N. is an employee of Oxford Nanopore Technologies; A.F. is an employee of DNAnexus; C.-S.C. is an employee of Sema4 OpCo Inc.; N.-C.C. is an employee of Exai Bio; L.F.P. receives research support from Genetech; F.J.S. receives research support from Pacific Biosciences, Oxford Nanopore Technologies, Illumina, and Genetech; K.S. is an employee of Google LLC and owns Alphabet stock as part of the standard compensation package; W.T. has two patents (8,748,091 and 8,394,584) licensed to Oxford Nanopore Technologies; E.E.E. is a scientific advisory board member of Variant Bio, Inc.