T2T Consortium papers​​

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• Telomere-to-telomere assembly of a complete human X chromosome (Miga et al., Nature, 2020)

• The structure, function and evolution of a complete human chromosome 8 (Logsdon et al., Nature, 2021)

• The complete sequence of a human genome (Nurk et al., Science, 2022)

• Complete genomic and epigenetic maps of human centromeres (Altemose et al., Science, 2022)

• Epigenetic patterns in a complete human genome (Gershman et al., Science, 2022)

• The complete sequence of a human Y chromosome (Rhie et al., Nature, 2023)

• The variation and evolution of complete human centromeres (Logsdon et al., Nature, 2024)

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HGSVC consortium papers

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• Haplotype-resolved diverse human genomes and integrated analysis of structural variation (Ebert et al., Science, 2021)

• Assembly of 43 diverse human Y chromosomes reveals extensive complexity and variation (Hallast et al., Nature, 2023)
   

HPRC papers

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• Semi-automated assembly of high-quality diploid human reference genomes (Jarvis et al., Nature, 2022)

• A draft human pangenome reference (Liao et al., Nature, 2023)

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Tools/methods papers​

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• Telomere-to-telomere assembly of diploid chromosomes with Verkko (Rautiainen et al., Nature Biotechnology, 2023)

• Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm (Cheng et al., Nature Methods, 2021)

• GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads (Dishuck, Bioinformatics, 2023)

• Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies (McCartney et al., Nature Methods, 2022)

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Github repos​

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• Verkko

• hifiasm

• minimap2

• Winnowmap

• RepeatMasker

• HumAS-HMMER

• StringDecomposer

• FLAGGER

• StainedGlass

• NucFreq

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Reviews

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• Long-read human genome sequencing and its applications (Logsdon et al., Nat Rev Gen, 2020)

• The dynamic structure and rapid evolution of human centromeric satellite DNA (Logsdon and Eichler, Genes, 2022)

• Variation and evolution of human centromeres: a field guide and perspective (Miga and Alexandrov, Annu Rev Genet, 2021)

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HAC papers

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• Human artificial chromosomes that bypass centromeric DNA (Logsdon et al., Cell, 2019)

• Efficient formation of single-copy human artificial chromosomes (Gambogi et al., Science, 2024)

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