scholarly journals Integration of string and de Bruijn graphs for genome assembly

2016 ◽  
Vol 32 (9) ◽  
pp. 1301-1307 ◽  
Author(s):  
Yao-Ting Huang ◽  
Chen-Fu Liao
Keyword(s):  
Genome Assembly ◽  
De Bruijn Graphs ◽  
De Bruijn

scholarly journals How to apply de Bruijn graphs to genome assembly

2011 ◽  
Vol 29 (11) ◽  
pp. 987-991 ◽  
Author(s):  
Phillip E C Compeau ◽  
Pavel A Pevzner ◽  
Glenn Tesler
Keyword(s):  
Genome Assembly ◽  
De Bruijn Graphs ◽  
De Bruijn

scholarly journals Assembly of Long Error-Prone Reads Using de Bruijn Graphs

2016 ◽  
Author(s):  
Yu Lin ◽  
Jeffrey Yuan ◽  
Mikhail Kolmogorov ◽  
Max W. Shen ◽  
Pavel A. Pevzner
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Genome Assembly ◽  
State Of The Art ◽  
De Bruijn Graph ◽  
Consensus Approach ◽  
De Bruijn Graphs ◽  
De Bruijn

AbstractThe recent breakthroughs in assembling long error-prone reads (such as reads generated by Single Molecule Real Time technology) were based on the overlap-layout-consensus approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the overlap-layout-consensus approach is the only practical paradigm for assembling long error-prone reads. Below we show how to generalize de Bruijn graphs to assemble long error-prone reads and describe the ABruijn assembler, which results in more accurate genome reconstructions than the existing state-of-the-art algorithms.

scholarly journals What do Eulerian and Hamiltonian cycles have to do with genome assembly?

2021 ◽  
Vol 17 (5) ◽  
pp. e1008928
Author(s):  
Paul Medvedev ◽  
Mihai Pop
Keyword(s):  
Genome Assembly ◽  
Linear Time ◽  
Hamiltonian Cycles ◽  
De Bruijn Graphs ◽  
Genome Reconstruction ◽  
Assembly Algorithm ◽  
A Genome ◽  
De Bruijn ◽  
Do So

Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively). This dichotomy is sometimes used to motivate the use of de Bruijn graphs in practice. In this paper, we explain that while de Bruijn graphs have indeed been very useful, the reason has nothing to do with the complexity of the Hamiltonian and Eulerian cycle problems. We give 2 arguments. The first is that a genome reconstruction is never unique and hence an algorithm for finding Eulerian or Hamiltonian cycles is not part of any assembly algorithm used in practice. The second is that even if an arbitrary genome reconstruction was desired, one could do so in linear time in both the Eulerian and Hamiltonian paradigms.

scholarly journals Assembly of long error-prone reads using de Bruijn graphs

2016 ◽  
Vol 113 (52) ◽  
pp. E8396-E8405 ◽  
Author(s):  
Yu Lin ◽  
Jeffrey Yuan ◽  
Mikhail Kolmogorov ◽  
Max W. Shen ◽  
Mark Chaisson ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Bruijn Graph ◽  
De Bruijn Graphs ◽  
De Bruijn

The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

2012 ◽  
pp. 249-261 ◽  
Author(s):  
Nikolay Vyahhi ◽  
Alex Pyshkin ◽  
Son Pham ◽  
Pavel A. Pevzner
Keyword(s):  
Genome Assembly ◽  
De Bruijn Graphs ◽  
De Bruijn

scholarly journals Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era

2019 ◽  
Vol 7 (4) ◽  
pp. 278-292 ◽  
Author(s):  
Raffaella Rizzi ◽  
Stefano Beretta ◽  
Murray Patterson ◽  
Yuri Pirola ◽  
Marco Previtali ◽  
...  
Keyword(s):  
Big Data ◽  
Data Structures ◽  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly ◽  
De Bruijn Graphs ◽  
Overlap Graphs ◽  
De Bruijn

scholarly journals Combining De Bruijn Graphs, Overlap Graphs and Microassembly for De Novo Genome Assembly

2013 ◽  
Vol 13 (2(2)) ◽  
pp. 51-57 ◽  
Author(s):  
A. A. Sergushichev ◽  
◽  
A. V. Alexandrov ◽  
S. V. Kazakov ◽  
F. N. Tsarev ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly ◽  
De Bruijn Graphs ◽  
Overlap Graphs ◽  
De Bruijn

scholarly journals Buffering Updates Enables Efficient Dynamic de Bruijn Graphs

2021 ◽  
Author(s):  
Jarno Alanko ◽  
Bahar Alipanahi ◽  
Jonathen Settle ◽  
Christina Boucher ◽  
Travis Gagie
Keyword(s):  
De Bruijn Graphs ◽  
De Bruijn
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