2023
Gaps and complex structurally variant loci in phased genome assemblies
Porubsky D, Vollger M, Harvey W, Rozanski A, Ebert P, Hickey G, Hasenfeld P, Sanders A, Stober C, Consortium H, Korbel J, Paten B, Marschall T, Eichler E, Abel H, Antonacci-Fulton L, Asri M, Baid G, Baker C, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson M, Chang P, Chang X, Cheng H, Chu J, Cody S, Colonna V, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler E, Eizenga J, Fairley S, Fedrigo O, Felsenfeld A, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton R, Gao Y, Garg S, Garrison E, Garrison N, Giron C, Green R, Groza C, Guarracino A, Haggerty L, Hall I, Harvey W, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis E, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Li H, Liao W, Lu S, Lu T, Lucas J, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin F, McCartney A, McDaniel J, Miga K, Mitchell M, Monlong J, Mountcastle J, Munson K, Mwaniki M, Nattestad M, Novak A, Nurk S, Olsen H, Olson N, Paten B, Pesout T, Phillippy A, Popejoy A, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Sibbesen J, Sirén J, Smith M, Sofia H, Tayoun A, Thibaud-Nissen F, Tomlinson C, Tricomi F, Villani F, Vollger M, Wagner J, Walenz B, Wang T, Wood J, Zimin A, Zook J. Gaps and complex structurally variant loci in phased genome assemblies. Genome Research 2023, 33: 496-510. PMID: 37164484, PMCID: PMC10234299, DOI: 10.1101/gr.277334.122.Peer-Reviewed Original ResearchConceptsProtein-coding genesGenome assemblyMbp of DNALinked-read dataLarge segmental duplicationsStrand-seqDiversity panelInversion polymorphismHaploid genomeSegmental duplicationsEuchromatic DNAMore haplotypesIdentical repeatsHaploid assembliesVariant lociDNAHaplotypesGenesFrequent expansionAssembly gapsImportant targetAssemblyHuman speciesHuman samplesMBP
2021
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng H, Concepcion G, Feng X, Zhang H, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 2021, 18: 170-175. PMID: 33526886, PMCID: PMC7961889, DOI: 10.1038/s41592-020-01056-5.Peer-Reviewed Original ResearchConceptsHaplotype-resolved de novo assembliesAssembly graphStudy of sequence variationHaplotype-resolved assembliesDe novo assemblyGraph-based assemblersConsensus copyHaplotype informationSequence readsHexaploid genomeTrio binningSequence variationHifiasmHeterozygous allelesHaplotypesGenomeCalifornia redwoodBinning algorithmAssemblyHexaploidAllelesCopy
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