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dc.contributor.authorBradnam, Keith R
dc.contributor.authorFass, Joseph N
dc.contributor.authorAlexandrov, Anton
dc.contributor.authorBaranay, Paul
dc.contributor.authorBechner, Michael
dc.contributor.authorBirol, Inanç
dc.contributor.authorBoisvert, Sébastien
dc.contributor.authorChapman, Jarrod A
dc.contributor.authorChapuis, Guillaume
dc.contributor.authorChikhi, Rayan
dc.contributor.authorChitsaz, Hamidreza
dc.contributor.authorChou, Wen-Chi
dc.contributor.authorCorbeil, Jacques
dc.contributor.authorDel Fabbro, Cristian
dc.contributor.authorDocking, T R
dc.contributor.authorDurbin, Richard
dc.contributor.authorEarl, Dent
dc.contributor.authorEmrich, Scott
dc.contributor.authorFedotov, Pavel
dc.contributor.authorFonseca, Nuno A
dc.contributor.authorGanapathy, Ganeshkumar
dc.contributor.authorGibbs, Richard A
dc.contributor.authorGnerre, Sante
dc.contributor.authorGodzaridis, Élénie
dc.contributor.authorGoldstein, Steve
dc.contributor.authorHaimel, Matthias
dc.contributor.authorHall, Giles
dc.contributor.authorHaussler, David
dc.contributor.authorHiatt, Joseph B
dc.contributor.authorHo, Isaac Y
dc.contributor.authorHoward, Jason
dc.contributor.authorHunt, Martin
dc.contributor.authorJackman, Shaun D
dc.contributor.authorJaffe, David B
dc.contributor.authorJarvis, Erich D
dc.contributor.authorJiang, Huaiyang
dc.contributor.authorKazakov, Sergey
dc.contributor.authorKersey, Paul J
dc.contributor.authorKitzman, Jacob O
dc.contributor.authorKnight, James R
dc.contributor.authorKoren, Sergey
dc.contributor.authorLam, Tak-Wah
dc.contributor.authorLavenier, Dominique
dc.contributor.authorLaviolette, François
dc.contributor.authorLi, Yingrui
dc.contributor.authorLi, Zhenyu
dc.contributor.authorLiu, Binghang
dc.contributor.authorLiu, Yue
dc.contributor.authorLuo, Ruibang
dc.contributor.authorMacCallum, Iain
dc.contributor.authorMacManes, Matthew D
dc.contributor.authorMaillet, Nicolas
dc.contributor.authorMelnikov, Sergey
dc.contributor.authorNaquin, Delphine
dc.contributor.authorNing, Zemin
dc.contributor.authorOtto, Thomas D
dc.contributor.authorPaten, Benedict
dc.contributor.authorPaulo, Octávio S
dc.contributor.authorPhillippy, Adam M
dc.contributor.authorPina-Martins, Francisco
dc.contributor.authorPlace, Michael
dc.contributor.authorPrzybylski, Dariusz
dc.contributor.authorQin, Xiang
dc.contributor.authorQu, Carson
dc.contributor.authorRibeiro, Filipe J
dc.contributor.authorRichards, Stephen
dc.contributor.authorRokhsar, Daniel S
dc.contributor.authorRuby, J G
dc.contributor.authorScalabrin, Simone
dc.contributor.authorSchatz, Michael C
dc.contributor.authorSchwartz, David C
dc.contributor.authorSergushichev, Alexey
dc.contributor.authorSharpe, Ted
dc.contributor.authorShaw, Timothy I
dc.contributor.authorShendure, Jay
dc.contributor.authorShi, Yujian
dc.contributor.authorSimpson, Jared T
dc.contributor.authorSong, Henry
dc.contributor.authorTsarev, Fedor
dc.contributor.authorVezzi, Francesco
dc.contributor.authorVicedomini, Riccardo
dc.contributor.authorVieira, Bruno M
dc.contributor.authorWang, Jun
dc.contributor.authorWorley, Kim C
dc.contributor.authorYin, Shuangye
dc.contributor.authorYiu, Siu-Ming
dc.contributor.authorYuan, Jianying
dc.contributor.authorZhang, Guojie
dc.contributor.authorZhang, Hao
dc.contributor.authorZhou, Shiguo
dc.contributor.authorKorf, Ian F
dc.date.accessioned2013-10-22T12:13:28Z
dc.date.available2013-10-22T12:13:28Z
dc.date.issued2013-07-22
dc.identifier.citationGigaScience. 2013 Jul 22;2(1):10
dc.identifier.urihttp://dx.doi.org/10.1186/2047-217X-2-10
dc.identifier.urihttp://hdl.handle.net/10724/19900
dc.description.abstractAbstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
dc.titleAssemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
dc.typeJournal Article
dc.date.updated2013-10-02T04:14:31Z
dc.description.versionPeer Reviewed
dc.language.rfc3066en
dc.rights.holderKeith R Bradnam et al.; licensee BioMed Central Ltd.


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