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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,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...,23 Mario Caccamo,26 Yingrui Li,29 David B. Jaffe,30 Richard E. Green,2 David Haussler,1,2,23 Ian Korf,3,32 and Benedict Paten1,2,33 1–32[Author affiliations appear at the end of the paper.] Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical...
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Resource: De novo assembly of human genomes with massively parallel short read sequencing
- Ruiqiang Li,
- Hongmei Zhu,
- Jue Ruan,
- Wubin Qian,
- Xiaodong Fang,
- Zhongbin Shi,
- Yingrui Li,
- Shengting Li,
- Gao Shan,
- Karsten Kristiansen,
- Songgang Li,
- Huanming Yang,
- Jian Wang,
- and Jun Wang
Genome Res. February 2010 20: 265-272; Published in Advance December 17, 2009, doi:10.1101/gr.097261.109
....9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. Footnotes ↵ 4 Corresponding...
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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,
- and İnanç Birol
Genome Res. June 2009 19: 1117-1123; Published in Advance February 27, 2009, doi:10.1101/gr.089532.108
....T. , et al. ( 2008 ) The complete of an individual by massively parallel DNA sequencing . Nature 452 : 872 – 876 . ↵ Zerbino, D.R. , Birney, E. ( 2008 ) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs . Genome Res. 18 : 821 – 829 . ↵ Zhang, Z. , Schwartz, S. , Wagner, L. , Miller...
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RESOURCE: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
- Daniel R. Zerbino and
- Ewan Birney
Genome Res. May 2008 18: 821-829; Published in Advance March 18, 2008, doi:10.1101/gr.074492.107
...– 2074 . ↵ Dohm, J.C. , Lottaz, C. , Borodina, T. , Himmelbauer, H. ( 2007 ) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing . Genome Res. 17 : 1697 – 1706 . ↵ Gross, J.L. , Yellen, J. ( 2004 ) Handbook of graph theory ( CRC Press LLC , Boca Raton, FL...
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Methods: De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae
- Josephine A. Reinhardt,
- David A. Baltrus,
- Marc T. Nishimura,
- William R. Jeck,
- Corbin D. Jones,
- and Jeffery L. Dangl
Genome Res. February 2009 19: 294-305; Published in Advance November 17, 2008, doi:10.1101/gr.083311.108
...contributed equally to this work. Abstract We developed a novel approach for de novo genome assembly using only sequence data from high-throughput short read sequencing technologies. By combining data generated from 454 Life Sciences (Roche) and Illumina (formerly known as Solexa sequencing...
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RESOURCE: De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer
- David Hernandez,
- Patrice François,
- Laurent Farinelli,
- Magne Østerås,
- and Jacques Schrenzel
Genome Res. May 2008 18: 802-809; Published in Advance March 10, 2008, doi:10.1101/gr.072033.107
.... , Himmelbauer, H. ( 2007 ) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing . Genome Res. 17 : 1697 – 1706 . ↵ Eisen, J.A. ( 2007 ) Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes . PLoS Biol. 5 : e82 , doi...
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RESOURCE: ALLPATHS: De novo assembly of whole-genome shotgun microreads
- Jonathan Butler,
- Iain MacCallum,
- Michael Kleber,
- Ilya A. Shlyakhter,
- Matthew K. Belmonte,
- Eric S. Lander,
- Chad Nusbaum,
- and David B. Jaffe
Genome Res. May 2008 18: 810-820; Published in Advance March 13, 2008, doi:10.1101/gr.7337908
...deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial, theoretical solution to the challenge of de novo assembly from whole-genome shotgun “microreads.” For 11 genomes of sizes up to 39 Mb, we...
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RESOURCE: De novo fragment assembly with short mate-paired reads: Does the read length matter?
- Mark J. Chaisson,
- Dumitru Brinza,
- and Pavel A. Pevzner
Genome Res. February 2009 19: 336-346; Published in Advance December 3, 2008, doi:10.1101/gr.079053.108
...). Simplifying the repeat graph by transforming mate-pairs into mate-reads Since the initial proposal to use mate-paired reads for shotgun sequencing ( Weber and Myers 1997 ), mate-paired reads have been considered essential to de novo sequencing. Although in the past the short-read mate-paired data have...
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Next-Generation DNA Sequencing/Review: The new paradigm of flow cell sequencing
- Robert A. Holt and
- Steven J.M. Jones
Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107
...rearrangements such as inversions and deletions, particularly where paired-end sequencing methods are deployed. De-novo assembly is an appealing application for flow cell sequencing but a challenging one for the short-read platforms. It is recognized that a contig accurately assembled from short reads can...

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