Journal ArticleDOI
The greedy path-merging algorithm for contig scaffolding
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TLDR
An efficient heuristic called the greedy-path merging algorithm for solving the Contig Scaffolding Problem is described, originally developed as a key component of the compartmentalized assembly strategy developed at Celera Genomics.Abstract:
Given a collection of contigs and mate-pairs. The Contig Scaffolding Problem is to order and orientate the given contigs in a manner that is consistent with as many mate-pairs as possible. This paper describes an efficient heuristic called the greedy-path merging algorithm for solving this problem. The method was originally developed as a key component of the compartmentalized assembly strategy developed at Celera Genomics. This interim approach was used at an early stage of the sequencing of the human genome to produce a preliminary assembly based on preliminary whole genome shotgun data produced at Celera and preliminary human contigs produced by the Human Genome Project.read more
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Journal ArticleDOI
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich,Sergey Nurk,Dmitry Antipov,Alexey Gurevich,Mikhail Dvorkin,Alexander S. Kulikov,Valery M. Lesin,Sergey I. Nikolenko,Son Pham,Andrey D. Prjibelski,Alexey V. Pyshkin,Alexander Sirotkin,Nikolay Vyahhi,Glenn Tesler,Max A. Alekseyev,Pavel A. Pevzner +15 more
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph.
Zhenyu Li,Yanxiang Chen,Desheng Mu,Jianying Yuan,Yujian Shi,Hao Zhang,Jun Gan,Nan Li,Xuesong Hu,Binghang Liu,Bicheng Yang,Wei Fan +11 more
TL;DR: A detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph is made, from how they match the Lander-Waterman model, to the required sequencing depth and reads length.
Journal ArticleDOI
Bioinformatics—an introduction for computer scientists
TL;DR: A bird's eye view of the basic concepts in molecular cell biology is provided, the nature of the existing data is outlined, and the kind of computer algorithms and techniques that are necessary to understand cell behavior are described.
Journal ArticleDOI
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
TL;DR: A novel heuristic algorithm, Pebble, which uses paired-end read information to resolve repeats and scaffold contigs to produce large-scale assemblies to extend the utility of short read only assemblies into large complex genomes.
References
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Journal ArticleDOI
DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
Book
Computers and Intractability: A Guide to the Theory of NP-Completeness
TL;DR: The second edition of a quarterly column as discussed by the authors provides a continuing update to the list of problems (NP-complete and harder) presented by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NP-Completeness,” W. H. Freeman & Co., San Francisco, 1979.
Journal ArticleDOI
Initial sequencing and analysis of the human genome.
Eric S. Lander,Lauren Linton,Bruce W. Birren,Chad Nusbaum,Michael C. Zody,Jennifer Baldwin,Keri Devon,Ken Dewar,Michael Doyle,William Fitzhugh,Roel Funke,Diane Gage,Katrina Harris,Andrew Heaford,John Howland,Lisa Kann,Jessica A. Lehoczky,Rosie Levine,Paul A. McEwan,Kevin McKernan,James Meldrim,Jill P. Mesirov,Cher Miranda,William Morris,Jerome Naylor,Christina Raymond,Mark Rosetti,Ralph Santos,Andrew Sheridan,Carrie Sougnez,Nicole Stange-Thomann,Nikola Stojanovic,Aravind Subramanian,Dudley Wyman,Jane Rogers,John Sulston,R Ainscough,Stephan Beck,David Bentley,John Burton,C M Clee,Nigel P. Carter,Alan Coulson,Rebecca Deadman,Panos Deloukas,Andrew Dunham,Ian Dunham,Richard Durbin,Lisa French,Darren Grafham,Simon G. Gregory,Tim Hubbard,Sean Humphray,Adrienne Hunt,Matthew Jones,Christine Lloyd,Amanda McMurray,Lucy Matthews,Simon Mercer,Sarah Milne,James C. Mullikin,Andrew J. Mungall,Robert W. Plumb,Mark T. Ross,Ratna Shownkeen,Sarah Sims,Robert H. Waterston,Richard K. Wilson,LaDeana W. Hillier,John Douglas Mcpherson,Marco A. Marra,Elaine R. Mardis,Lucinda Fulton,Asif T. Chinwalla,Kymberlie H. Pepin,Warren Gish,Stephanie L. Chissoe,Michael C. Wendl,Kim D. Delehaunty,Tracie L. Miner,Andrew Delehaunty,Jason B. Kramer,Lisa Cook,Robert S. Fulton,Douglas L. Johnson,Patrick Minx,Sandra W. Clifton,Trevor Hawkins,Elbert Branscomb,Paul Predki,Paul G. Richardson,Sarah Wenning,Tom Slezak,Norman A. Doggett,Jan Fang Cheng,Anne S. Olsen,Susan Lucas,Christopher J. Elkin,Edward Uberbacher,Marvin Frazier,Richard A. Gibbs,Donna M. Muzny,Steven E. Scherer,John Bouck,Erica Sodergren,Kim C. Worley,Catherine M. Rives,James H. Gorrell,Michael L. Metzker,Susan L. Naylor,Raju Kucherlapati,David L. Nelson,George M. Weinstock,Yoshiyuki Sakaki,Asao Fujiyama,Masahira Hattori,Tetsushi Yada,Atsushi Toyoda,Takehiko Itoh,Chiharu Kawagoe,Hidemi Watanabe,Yasushi Totoki,Todd D. Taylor,Jean Weissenbach,Roland Heilig,William Saurin,François Artiguenave,Philippe Brottier,Thomas Brüls,Eric Pelletier,Catherine Robert,Patrick Wincker,André Rosenthal,Matthias Platzer,Gerald Nyakatura,Stefan Taudien,Andreas Rump,Douglas R. Smith,Lynn Doucette-Stamm,Marc Rubenfield,Keith Weinstock,Mei Lee Hong,Joann Dubois,Huanming Yang,Jun Yu,Jian Wang,Guyang Huang,Jun Gu,Leroy Hood,Lee Rowen,Anup Madan,Shizen Qin,Ronald W. Davis,Nancy A. Federspiel,A. Pia Abola,Michael Proctor,Bruce A. Roe,Feng Chen,Huaqin Pan,Juliane Ramser,Hans Lehrach,Richard Reinhardt,W. Richard McCombie,Melissa De La Bastide,Neilay Dedhia,H. Blöcker,K. Hornischer,Gabriele Nordsiek,Richa Agarwala,L. Aravind,Jeffrey A. Bailey,Alex Bateman,Serafim Batzoglou,Ewan Birney,Peer Bork,Daniel G. Brown,Christopher B. Burge,Lorenzo Cerutti,Hsiu Chuan Chen,Deanna M. Church,Michele Clamp,Richard R. Copley,Tobias Doerks,Sean R. Eddy,Evan E. Eichler,Terrence S. Furey,James E. Galagan,James G. R. Gilbert,Cyrus L. Harmon,Yoshihide Hayashizaki,David Haussler,Henning Hermjakob,Karsten Hokamp,Wonhee Jang,L. Steven Johnson,Thomas A. Jones,Simon Kasif,Arek Kaspryzk,Scot Kennedy,W. James Kent,Paul Kitts,Eugene V. Koonin,Ian F Korf,David Kulp,Doron Lancet,Todd M. Lowe,Aoife McLysaght,Tarjei S. Mikkelsen,John V. Moran,Nicola Mulder,Victor J. Pollara,Chris P. Ponting,Greg Schuler,Jörg Schultz,Guy Slater,Arian F.A. Smit,Elia Stupka,Joseph Szustakowki,Danielle Thierry-Mieg,Jean Thierry-Mieg,Lukas Wagner,John W. Wallis,Raymond Wheeler,Alan Williams,Yuri I. Wolf,Kenneth H. Wolfe,Shiaw Pyng Yang,Ru Fang Yeh,Francis S. Collins,Mark S. Guyer,Jane Peterson,Adam Felsenfeld,Kris A. Wetterstrand,Richard M. Myers,Jeremy Schmutz,Mark Dickson,Jane Grimwood,David R. Cox,Maynard V. Olson,Rajinder Kaul,Christopher K. Raymond,Nobuyoshi Shimizu,Kazuhiko Kawasaki,Shinsei Minoshima,Glen A. Evans,Maria Athanasiou,Roger A. Schultz,Aristides Patrinos,Michael J. Morgan +248 more
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Book
Data Reduction and Error Analysis for the Physical Sciences
TL;DR: In this paper, Monte Carlo techniques are used to fit dependent and independent variables least squares fit to a polynomial least-squares fit to an arbitrary function fitting composite peaks direct application of the maximum likelihood.
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