2024
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Cheng H, Asri M, Lucas J, Koren S, Li H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nature Methods 2024, 21: 967-970. PMID: 38730258, PMCID: PMC11214949, DOI: 10.1038/s41592-024-02269-8.Peer-Reviewed Original Research
2023
A draft human pangenome reference
Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Sirén J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Garrison N, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson N, Popejoy A, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Smith M, Sofia H, Abou Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Walenz B, Wood J, Zimin A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Wang T, Jarvis E, Miga K, Garrison E, Marschall T, Hall I, Li H, Paten B. A draft human pangenome reference. Nature 2023, 617: 312-324. PMID: 37165242, PMCID: PMC10172123, DOI: 10.1038/s41586-023-05896-x.Peer-Reviewed Original Research
2022
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis E, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger M, Porubsky D, Cheng H, Asri M, Logsdon G, Carnevali P, Chaisson M, Chin C, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton R, Fulton L, Garg S, Gerton J, Ghurye J, Granat A, Green R, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger E, Jain M, Kirsche M, Kolmogorov M, Korbel J, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell M, McDaniel J, Nie F, Olsen H, Olson N, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg S, Sanders A, Schatz M, Schmitt A, Schneider V, Selvaraj S, Shafin K, Shumate A, Stitziel N, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin A, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook J, Eichler E, Phillippy A, Paten B, Howe K, Miga K. Semi-automated assembly of high-quality diploid human reference genomes. Nature 2022, 611: 519-531. PMID: 36261518, PMCID: PMC9668749, DOI: 10.1038/s41586-022-05325-5.Peer-Reviewed Original ResearchConceptsDiploid genome assemblyGenome assemblyProtein-coding genesGlobal genetic variationCurrent human reference genomeDiploid human genomeHigh-quality assemblyAccurate long readsNon-synonymous amino acid changesHuman reference genomeAmino acid changesMost chromosomesReference assemblyReference genomeHuman genomeCentromeric regionsGenetic variationHigh diversityGenome sequencingLong readsSingle nucleotideGenomeAcid changesManual curationBiological genomesHaplotype-resolved assembly of diploid genomes without parental data
Cheng H, Jarvis E, Fedrigo O, Koepfli K, Urban L, Gemmell N, Li H. Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology 2022, 40: 1332-1335. PMID: 35332338, PMCID: PMC9464699, DOI: 10.1038/s41587-022-01261-x.Peer-Reviewed Original Research
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