Browsing by Author "Earl, Dent"

Filter results by typing the first few letters
Now showing 1 - 2 of 2
  • Thumbnail Image
    ItemOpen Access
    Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
    (Gigascience, 2013-07-22) Bradnam, Keith R; Fass, Joseph N; Alexandrov, Anton; Baranay, Paul; Bechner, Michael; Birol, Inanç; Boisvert, Sébastien; Chapman, Jarrod A; Chapuis, Guillaume; Chikhi, Rayan; Chitsaz, Hamidreza; Chou, Wen-Chi; Corbeil, Jacques; Del Fabbro, Cristian; Docking, T Roderick; Durbin, Richard; Earl, Dent; Emrich, Scott; Fedotov, Pavel; Fonseca, Nuno A; Ganapathy, Ganeshkumar; Gibbs, Richard A; Gnerre, Sante; Godzaridis, Elénie; Goldstein, Steve; Haimel, Matthias; Hall, Giles; Haussler, David; Hiatt, Joseph B; Ho, Isaac Y; Howard, Jason; Hunt, Martin; Jackman, Shaun D; Jaffe, David B; Jarvis, Erich D; Jiang, Huaiyang; Kazakov, Sergey; Kersey, Paul J; Kitzman, Jacob O; Knight, James R; Koren, Sergey; Lam, Tak-Wah; Lavenier, Dominique; Laviolette, François; Li, Yingrui; Li, Zhenyu; Liu, Binghang; Liu, Yue; Luo, Ruibang; Maccallum, Iain; Macmanes, Matthew D; Maillet, Nicolas; Melnikov, Sergey; Naquin, Delphine; Ning, Zemin; Otto, Thomas D; Paten, Benedict; Paulo, Octávio S; Phillippy, Adam M; Pina-Martins, Francisco; Place, Michael; Przybylski, Dariusz; Qin, Xiang; Qu, Carson; Ribeiro, Filipe J; Richards, Stephen; Rokhsar, Daniel S; Ruby, J Graham; Scalabrin, Simone; Schatz, Michael C; Schwartz, David C; Sergushichev, Alexey; Sharpe, Ted; Shaw, Timothy I; Shendure, Jay; Shi, Yujian; Simpson, Jared T; Song, Henry; Tsarev, Fedor; Vezzi, Francesco; Vicedomini, Riccardo; Vieira, Bruno M; Wang, Jun; Wang, Jun; Worley, Kim C; Yin, Shuangye; Yiu, Siu-Ming; Yuan, Jianying; Zhang, Guojie; Zhang, Hao; Zhou, Shiguo; Korf, Ian F
    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.
  • Thumbnail Image
    ItemOpen Access
    Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
    (Science, 2014-12-12) Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A
    To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.