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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

  • Valerie A. Schneider
  • Tina Graves-Lindsay
  • Kerstin Howe
  • Nathan Bouk
  • Hsiu-Chuan Chen
  • Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
  • ... [+29 authors] ...,
  • Richard K. Wilson
  • Paul Flicek
  • Evan E. Eichler
  • Deanna M. Church
  • First Published April 10, 2017
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Alignathon: a competitive assessment of whole-genome alignment methods

  • Dent Earl
  • Ngan Nguyen
  • Glenn Hickey
  • Robert S. Harris
  • Stephen Fitzgerald
  • Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian J. Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero William James Kent Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame
  • ... [+17 authors] ...,
  • Michael Brudno
  • Inna Dubchak
  • David Haussler
  • Benedict Paten
  • First Published October 1, 2014
Resource

Assemblathon 1: A competitive assessment of de novo short read assembly methods

  • Dent Earl
  • Keith Bradnam
  • John St. John
  • Aaron Darling
  • Dawei Lin
  • Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
  • ... [+62 authors] ...,
  • Richard E. Green
  • David Haussler
  • Ian Korf
  • Benedict Paten
  • First Published September 16, 2011
Resource

Cactus: Algorithms for genome multiple sequence alignment

  • Benedict Paten
  • Dent Earl
  • Ngan Nguyen
  • Mark Diekhans
  • Daniel Zerbino
  • David Haussler
  • First Published June 10, 2011
Resource

ABySS: A parallel assembler for short read sequence data

  • Jared T. Simpson
  • Kim Wong
  • Shaun D. Jackman
  • Jacqueline E. Schein
  • Steven J.M. Jones
  • İnanç Birol
  • First Published February 27, 2009
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