The complete sequence of a human genome

Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

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     Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V, breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics. 36, 1260–1261 (2020 ).

     Not in our library10.1093/bioinformatics/btz681

105. 105.

     Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, Devine SE, Sanders AD, Lee C, Chaisson MJP, Korbel JO, Eichler EE, Marschall T, Human Genome Structural Variation Consortium, Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat. Biotechnol 39, 302–308 (2021 ).

     Not in our library10.1038/s41587-020-0719-5

106. 106.
     HiGlass: web-based visual exploration and analysis of genome interaction maps · 2018

     No notice
107. 107.

     Krishnakumar R, Sinha A, Bird SW, Jayamohan H, Edwards HS, Schoeniger JS, Patel KD, Branda SS, Bartsch MS, Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias. Sci. Rep 8, 3159 (2018 ).

     Not in our library10.1038/s41598-018-21484-w

108. 108.

     Uralsky LI, Shepelev VA, Alexandrov AA, Yurov YB, Rogaev EI, Alexandrov IA, Classification and monomer-by-monomer annotation dataset of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly. Data Brief. 24, 103708 (2019 ).

     Not in our library10.1016/j.dib.2019.103708

109. 109.
     nhmmer: DNA homology search with profile HMMs · 2013

     No notice
110. 110.

     Vaser R, Sović I, Nagarajan N, Šikić M, Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017 ).

     Not in our library10.1101/gr.214270.116

111. 111.
     karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data · 2017

     No notice
112. 112.

     Harris RS, thesis, Pennsylvania State University, USA (2007 ).

     Not in our library

113. 113.

     Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D, Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 21, 1512–1528 (2011 ).

     Not in our library10.1101/gr.123356.111

114. 114.
     Transcriptome assembly from long-read RNA-seq alignments with StringTie2 · 2019

     No notice
115. 115.

     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 ).

     Not in our library10.1093/bioinformatics/btn013

116. 116.

     Miller CA, Walker JR, Jensen TL, Hooper WF, Fulton RS, Painter JS, Sekeres MA, Ley TJ, Spencer DH, Goll JB, Walter MJ, Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence. bioRxiv (2021 ), doi:.

     Not in our library10.1101/2021.05.07.442430

117. 117.
     GenMap: ultra-fast computation of genome mappability · 2020

     No notice
118. 118.

     Katoh K, Standley DM, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol 30, 772–780 (2013 ).

     Not in our library10.1093/molbev/mst010

119. 119.

     Kumar S, Stecher G, Li M, Knyaz C, Tamura K, MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol. Biol. Evol 35, 1547–1549 (2018 ).

     Not in our library10.1093/molbev/msy096

120. 120.

     Saitou N, Nei M, The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol 4, 406–425 (1987 ).

     Not in our library10.1093/oxfordjournals.molbev.a040454

121. 121.

     Kimura M, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol 16, 111–120 (1980 ).

     Not in our library10.1007/bf01731581

122. 122.

     Stamatakis A, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30, 1312–1313 (2014 ).

     Not in our library10.1093/bioinformatics/btu033

123. 123.

     Nei M, Kumar S, Molecular evolution and phylogenetics (Oxford university press, 2000 ).

     Not in our library

124. 124.

     Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C, Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 14, 417–419 (2017 ).

     Not in our library10.1038/nmeth.4197

125. 125.
     Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences · 2016

     No notice
126. 126.

     Delcher AL, Phillippy A, Carlton J, Salzberg SL, MUMmer: comparative applications Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30 (2002 ), pp. 2478–2483.

     Not in our library10.1093/nar/30.11.2478

127. 127.

     Ghareghani M, Porubskỳ D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T, Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. Bioinformatics. 34, i115–i123 (2018 ).

     Not in our library10.1093/bioinformatics/bty290

128. 128.

     Cheng H, Concepcion GT, Feng X, Zhang H, Li H, Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021 ).

     Not in our library10.1038/s41592-020-01056-5

Cited by papers we hold 40

• Complex genetic variation in nearly complete human genomes · 2025
  Corrected
• The UCSC Genome Browser database: 2026 update · 2025
  No notice
• Utility of long-read sequencing for All of Us · 2024
  No notice
• The complex polyploid genome architecture of sugarcane · 2024
  No notice
• The variation and evolution of complete human centromeres · 2024
  No notice
• New clinical trial design in precision medicine: discovery, development and direction · 2024
  No notice
• CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions · 2024
  No notice
• GENCODE 2025: reference gene annotation for human and mouse · 2024
  No notice
• Whole genome sequencing in clinical practice · 2024
  No notice
• NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads · 2024
  No notice
• A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation · 2024
  No notice
• Multi-Omics Profiling for Health · 2023
  No notice
• quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification · 2023
  No notice
• Evolutionary analysis of a complete chicken genome · 2023
  No notice
• Enzyme-less nanopore detection of post-translational modifications within long polypeptides · 2023
  No notice
• A complete telomere-to-telomere assembly of the maize genome · 2023
  No notice
• compleasm: a faster and more accurate reimplementation of BUSCO · 2023
  No notice
• The complete reference genome for grapevine ( Vitis vinifera L.) genetics and breeding · 2023
  No notice
• Major data analysis errors invalidate cancer microbiome findings · 2023
  No notice
• A draft human pangenome reference · 2023
  No notice

and 20 more

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.