scholarly journals Integrating long-range connectivity information into de Bruijn graphs

2018 ◽  
Vol 34 (15) ◽  
pp. 2556-2565 ◽  
Author(s):  
Isaac Turner ◽  
Kiran V Garimella ◽  
Zamin Iqbal ◽  
Gil McVean
Keyword(s):  
Long Range ◽  
De Bruijn Graphs ◽  
Connectivity Information ◽  
De Bruijn

scholarly journals Integrating long-range connectivity information into de Bruijn graphs

2017 ◽  
Author(s):  
Isaac Turner ◽  
Kiran V Garimella ◽  
Zamin Iqbal ◽  
Gil McVean
Keyword(s):  
Data Structure ◽  
Long Range ◽  
De Bruijn Graph ◽  
Sequencing Data ◽  
Genomic Context ◽  
De Bruijn Graphs ◽  
Connectivity Information ◽  
String Graph ◽  
Free Data ◽  
De Bruijn

AbstractMotivationThe de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input.ResultsWe present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both the de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterise the genomic context of drug-resistance genes.AvailabilityLinked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, available under the MIT license at https://github.com/mcvean/[email protected].

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

scholarly journals Matching preclusion and conditional edge-fault Hamiltonicity of binary de Bruijn graphs

2017 ◽  
Vol 233 ◽  
pp. 104-117 ◽  
Author(s):  
Ruizhi Lin ◽  
Heping Zhang
Keyword(s):  
De Bruijn Graphs ◽  
De Bruijn

scholarly journals Cartesian products of graphs as subgraphs of de Bruijn graphs of dimension at least three

1997 ◽  
Vol 79 (1-3) ◽  
pp. 3-34 ◽  
Author(s):  
Thomas Andreae ◽  
Martin Hintz ◽  
Michael Nölle ◽  
Gerald Schreiber ◽  
Gerald W. Schuster ◽  
...  
Keyword(s):  
Cartesian Products ◽  
De Bruijn Graphs ◽  
De Bruijn ◽  
Cartesian Products Of Graphs

scholarly journals On the Representation of de Bruijn Graphs

2014 ◽  
pp. 35-55 ◽  
Author(s):  
Rayan Chikhi ◽  
Antoine Limasset ◽  
Shaun Jackman ◽  
Jared T. Simpson ◽  
Paul Medvedev
Keyword(s):  
De Bruijn Graphs ◽  
De Bruijn

Embeddings of Hypercubes and Grids into de Bruijn Graphs

1994 ◽  
Vol 23 (1) ◽  
pp. 104-111 ◽  
Author(s):  
M.C. Heydemann ◽  
J. Opatrny ◽  
D. Sotteau
Keyword(s):  
De Bruijn Graphs ◽  
De Bruijn
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