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dc.contributor.authorRhie, Arangen
dc.contributor.authorMcCarthy, Shaneen
dc.contributor.authorFedrigo, Olivieren
dc.contributor.authorDamas, Joanaen
dc.contributor.authorFormenti, Giulioen
dc.contributor.authorKoren, Sergeyen
dc.contributor.authorUliano-Silva, Marcelaen
dc.contributor.authorChow, Williamen
dc.contributor.authorFungtammasan, Arkarachaien
dc.contributor.authorKim, Juwanen
dc.contributor.authorLee, Chulen
dc.contributor.authorKo, Byung Juneen
dc.contributor.authorChaisson, Marken
dc.contributor.authorGedman, Gregory Len
dc.contributor.authorCantin, Lindsey Jen
dc.contributor.authorThibaud-Nissen, Francoiseen
dc.contributor.authorHaggerty, Leanneen
dc.contributor.authorBista, Ilianaen
dc.contributor.authorSmith, Michelleen
dc.contributor.authorHaase, Bettinaen
dc.contributor.authorMountcastle, Jacquelynen
dc.contributor.authorWinkler, Sylkeen
dc.contributor.authorPaez, Sadyeen
dc.contributor.authorHoward, Jasonen
dc.contributor.authorVernes, Sonja Cen
dc.contributor.authorLama, Tanya Men
dc.contributor.authorGrutzner, Franken
dc.contributor.authorWarren, Wesley Cen
dc.contributor.authorBalakrishnan, Christopher Nen
dc.contributor.authorBurt, Daveen
dc.contributor.authorGeorge, Julia Men
dc.contributor.authorBiegler, Matthew Ten
dc.contributor.authorIorns, Daviden
dc.contributor.authorDigby, Andrewen
dc.contributor.authorEason, Darylen
dc.contributor.authorRobertson, Bruceen
dc.contributor.authorEdwards, Tayloren
dc.contributor.authorWilkinson, Marken
dc.contributor.authorTurner, Georgeen
dc.contributor.authorMeyer, Axelen
dc.contributor.authorKautt, Andreas Fen
dc.contributor.authorFranchini, Paoloen
dc.contributor.authorDetrich, H Williamen
dc.contributor.authorSvardal, Hannesen
dc.contributor.authorWagner, Maximilianen
dc.contributor.authorNaylor, Gavin JPen
dc.contributor.authorPippel, Martinen
dc.contributor.authorMalinsky, Milanen
dc.contributor.authorMooney, Marken
dc.contributor.authorSimbirsky, Mariaen
dc.contributor.authorHannigan, Brett Ten
dc.contributor.authorPesout, Trevoren
dc.contributor.authorHouck, Marlysen
dc.contributor.authorMisuraca, Annen
dc.contributor.authorKingan, Sarah Ben
dc.contributor.authorHall, Richarden
dc.contributor.authorKronenberg, Zeven
dc.contributor.authorSović, Ivanen
dc.contributor.authorDunn, Christopheren
dc.contributor.authorNing, Zeminen
dc.contributor.authorHastie, Alexen
dc.contributor.authorLee, Joyceen
dc.contributor.authorSelvaraj, Siddarthen
dc.contributor.authorGreen, Richard Een
dc.contributor.authorPutnam, Nicholas Hen
dc.contributor.authorGut, Ivoen
dc.contributor.authorGhurye, Jayen
dc.contributor.authorGarrison, Eriken
dc.contributor.authorSims, Yingen
dc.contributor.authorCollins, Joannaen
dc.contributor.authorPelan, Sarahen
dc.contributor.authorTorrance, Jamesen
dc.contributor.authorTracey, Alanen
dc.contributor.authorWood, Jonathanen
dc.contributor.authorDagnew, Robel Een
dc.contributor.authorGuan, Dengfengen
dc.contributor.authorLondon, Sarah Een
dc.contributor.authorClayton, David Fen
dc.contributor.authorMello, Claudio Ven
dc.contributor.authorFriedrich, Samantha Ren
dc.contributor.authorLovell, Peter Ven
dc.contributor.authorOsipova, Ekaterinaen
dc.contributor.authorAl-Ajli, Farooq Oen
dc.contributor.authorSecomandi, Simonaen
dc.contributor.authorKim, Heebalen
dc.contributor.authorTheofanopoulou, Constantinaen
dc.contributor.authorHiller, Michaelen
dc.contributor.authorZhou, Yangen
dc.contributor.authorHarris, Robert Sen
dc.contributor.authorMakova, Kateryna Den
dc.contributor.authorMedvedev, Paulen
dc.contributor.authorHoffman, Jinnaen
dc.contributor.authorMasterson, Patricken
dc.contributor.authorClark, Karenen
dc.contributor.authorMartin, Fergalen
dc.contributor.authorHowe, Kevinen
dc.contributor.authorFlicek, Paulen
dc.contributor.authorWalenz, Brian Pen
dc.contributor.authorKwak, Woorien
dc.contributor.authorClawson, Hiramen
dc.contributor.authorDiekhans, Marken
dc.contributor.authorNassar, Luisen
dc.contributor.authorPaten, Benedicten
dc.contributor.authorKraus, Robert HSen
dc.contributor.authorCrawford, Andrew Jen
dc.contributor.authorGilbert, M Thomas Pen
dc.contributor.authorZhang, Guojieen
dc.contributor.authorVenkatesh, Byrappaen
dc.contributor.authorMurphy, Robert Wen
dc.contributor.authorKoepfli, Klaus-Peteren
dc.contributor.authorShapiro, Bethen
dc.contributor.authorJohnson, Warren Een
dc.contributor.authorDi Palma, Federicaen
dc.contributor.authorMarques-Bonet, Tomasen
dc.contributor.authorTeeling, Emma Cen
dc.contributor.authorWarnow, Tandyen
dc.contributor.authorGraves, Jennifer Marshallen
dc.contributor.authorRyder, Oliver Aen
dc.contributor.authorHaussler, Daviden
dc.contributor.authorO'Brien, Stephen Jen
dc.contributor.authorKorlach, Jonasen
dc.contributor.authorLewin, Harris Aen
dc.contributor.authorHowe, Kerstinen
dc.contributor.authorMyers, Eugene Wen
dc.contributor.authorDurbin, Richarden
dc.contributor.authorPhillippy, Adam Men
dc.contributor.authorJarvis, Erich Den
dc.date.accessioned2021-07-05T13:32:07Z
dc.date.available2021-07-05T13:32:07Z
dc.date.issued2021-04-28en
dc.identifier.issn0028-0836
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/324784
dc.description.abstractHigh-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from applying the same sequencing data types and assembly algorithms across 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes, and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are remaining major sources of error in assemblies. Our new assemblies correct substantial errors and add missing sequence in some of the best historical reference genomes. They reveal new biological discoveries in gene family evolution, vertebrate chromosome evolution, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions, which were missing from prior short-read based assemblies. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.publisherNature Research
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleTowards complete and error-free genome assemblies of all vertebrate species.en
dc.typeArticle
prism.endingPage746
prism.issueIdentifier7856en
prism.publicationDate2021en
prism.publicationNameNatureen
prism.startingPage737
prism.volume592en
dc.identifier.doi10.17863/CAM.72237
dcterms.dateAccepted2021-03-12en
rioxxterms.versionofrecord10.1038/s41586-021-03451-0en
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2021-04-28en
dc.contributor.orcidRhie, Arang [0000-0002-9809-8127]
dc.contributor.orcidMcCarthy, Shane [0000-0002-2715-4187]
dc.contributor.orcidFedrigo, Olivier [0000-0002-6450-7551]
dc.contributor.orcidFormenti, Giulio [0000-0002-7554-5991]
dc.contributor.orcidKoren, Sergey [0000-0002-1472-8962]
dc.contributor.orcidUliano-Silva, Marcela [0000-0001-6723-4715]
dc.contributor.orcidChow, William [0000-0002-9056-201X]
dc.contributor.orcidThibaud-Nissen, Francoise [0000-0003-4957-7807]
dc.contributor.orcidMountcastle, Jacquelyn [0000-0003-1078-4905]
dc.contributor.orcidWinkler, Sylke [0000-0002-0915-3316]
dc.contributor.orcidHoward, Jason [0000-0003-3265-5127]
dc.contributor.orcidVernes, Sonja C [0000-0003-0305-4584]
dc.contributor.orcidGrutzner, Frank [0000-0002-3088-7314]
dc.contributor.orcidBalakrishnan, Christopher N [0000-0002-0788-0659]
dc.contributor.orcidBurt, Dave [0000-0002-9991-1028]
dc.contributor.orcidGeorge, Julia M [0000-0001-6194-6914]
dc.contributor.orcidDigby, Andrew [0000-0002-1870-8811]
dc.contributor.orcidRobertson, Bruce [0000-0002-5348-2731]
dc.contributor.orcidEdwards, Taylor [0000-0002-7235-6175]
dc.contributor.orcidMeyer, Axel [0000-0002-0888-8193]
dc.contributor.orcidKautt, Andreas F [0000-0001-7792-0735]
dc.contributor.orcidFranchini, Paolo [0000-0002-8184-1463]
dc.contributor.orcidDetrich, H William [0000-0002-0783-4505]
dc.contributor.orcidPippel, Martin [0000-0002-8134-5929]
dc.contributor.orcidMalinsky, Milan [0000-0002-1462-6317]
dc.contributor.orcidKingan, Sarah B [0000-0002-4900-0189]
dc.contributor.orcidHall, Richard [0000-0001-6490-8227]
dc.contributor.orcidDunn, Christopher [0000-0002-0601-3254]
dc.contributor.orcidLee, Joyce [0000-0002-3492-1102]
dc.contributor.orcidPutnam, Nicholas H [0000-0002-1315-782X]
dc.contributor.orcidGut, Ivo [0000-0001-7219-632X]
dc.contributor.orcidTracey, Alan [0000-0002-4805-9058]
dc.contributor.orcidGuan, Dengfeng [0000-0002-6376-3940]
dc.contributor.orcidLondon, Sarah E [0000-0002-7839-2644]
dc.contributor.orcidClayton, David F [0000-0002-6395-3488]
dc.contributor.orcidMello, Claudio V [0000-0002-9826-8421]
dc.contributor.orcidFriedrich, Samantha R [0000-0003-0570-6080]
dc.contributor.orcidOsipova, Ekaterina [0000-0002-6769-7223]
dc.contributor.orcidAl-Ajli, Farooq O [0000-0002-4692-7106]
dc.contributor.orcidSecomandi, Simona [0000-0001-8597-6034]
dc.contributor.orcidKim, Heebal [0000-0003-3064-1303]
dc.contributor.orcidTheofanopoulou, Constantina [0000-0003-2014-7563]
dc.contributor.orcidZhou, Yang [0000-0003-1247-5049]
dc.contributor.orcidMartin, Fergal [0000-0002-1672-050X]
dc.contributor.orcidFlicek, Paul [0000-0002-3897-7955]
dc.contributor.orcidWalenz, Brian P [0000-0001-8431-1428]
dc.contributor.orcidDiekhans, Mark [0000-0002-0430-0989]
dc.contributor.orcidPaten, Benedict [0000-0001-8863-3539]
dc.contributor.orcidCrawford, Andrew J [0000-0003-3153-6898]
dc.contributor.orcidGilbert, M Thomas P [0000-0002-5805-7195]
dc.contributor.orcidZhang, Guojie [0000-0001-6860-1521]
dc.contributor.orcidVenkatesh, Byrappa [0000-0003-3620-0277]
dc.contributor.orcidShapiro, Beth [0000-0002-2733-7776]
dc.contributor.orcidJohnson, Warren E [0000-0002-5954-186X]
dc.contributor.orcidMarques-Bonet, Tomas [0000-0002-5597-3075]
dc.contributor.orcidTeeling, Emma C [0000-0002-3309-1346]
dc.contributor.orcidRyder, Oliver A [0000-0003-2427-763X]
dc.contributor.orcidHaussler, David [0000-0003-1533-4575]
dc.contributor.orcidKorlach, Jonas [0000-0003-3047-4250]
dc.contributor.orcidLewin, Harris A [0000-0002-1043-7287]
dc.contributor.orcidHowe, Kerstin [0000-0003-2237-513X]
dc.contributor.orcidMyers, Eugene W [0000-0002-6580-7839]
dc.contributor.orcidDurbin, Richard [0000-0002-9130-1006]
dc.contributor.orcidPhillippy, Adam M [0000-0003-2983-8934]
dc.contributor.orcidJarvis, Erich D [0000-0001-8931-5049]
dc.identifier.eissn1476-4687
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idWellcome Trust (unknown)


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International