Results 41 to 50 of about 2,351 (162)
PLoS Computational Biology, 2021 Graphs such as de Bruijn graphs and OLC (overlap-layout-consensus) graphs have been widely adopted for the de novo assembly of genomic short reads. This work studies another important problem in the field: how graphs can be used for high-performance ...
Yuansheng Liu, Jinyan Li
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BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
Genome Biology, 2021 BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs.
Nina Luhmann +2 more
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RResolver: efficient short-read repeat resolution within ABySS
BMC Bioinformatics, 2022 Background De novo genome assembly is essential to modern genomics studies. As it is not biased by a reference, it is also a useful method for studying genomes with high variation, such as cancer genomes.
Vladimir Nikolić +7 more
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Bisecting de Bruijn and Kautz graphs
Discrete Applied Mathematics, 1998 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
José D. P. Rolim +3 more
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Practical dynamic de Bruijn graphs [PDF]
Bioinformatics, 2018 Abstract Motivation The de Bruijn graph is fundamental to the analysis of next generation sequencing data and so, as datasets of DNA reads grow rapidly, it becomes more important to represent de Bruijn graphs compactly while still supporting fast assembly. Previous implementations of compact de Bruijn
Victoria G. Crawford +4 more
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Colouring of cycles in the de bruijn graphs
Discussiones Mathematicae Graph Theory, 2000 The authors show that the problem of finding the family of all locally reducible factors in the binary de Bruijn graph of order \(k\) is equivalent to the problem of finding all colourings of the edges in the binary de Bruijn graph of order \(k-1\), where each vertex belongs to exactly two cycles of different colours.
Ewa Lazuka, Jerzy Zurawiecki
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Fully Dynamic de Bruijn Graphs [PDF]
, 2016 We present a space- and time-efficient fully dynamic implementation de Bruijn graphs, which can also support fixed-length jumbled pattern matching.
Djamal Belazzougui +3 more
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Spectra of the directed de Bruijn graphs(有向de Bruijn图的谱)
Zhejiang Daxue xuebao. Lixue ban, 2005 首先分析了n维d进位有向de Bruijn图B（d，n）(d≥2，n≥1)及其邻接矩阵A的结构，证明了从B（d，n）的顶点x到y只有一条长度为n的有向链，从而证得了An=J（其中J为dn×dn阶矩阵，且其全部元素均为1）.文章最后获得了有向de Bruijn图B（d，n）的谱，B(d,n)的特征值为0与d，且它们所对应的重数分别为dn-1和1.
YINJian-hong(殷剑宏)
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, 2012 We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers in a DNA sequence of length N has m edges, it can be represented in 4m+o(m) bits. This is much smaller than existing ones. The numbers of outgoing and incoming edges of a node are computed in constant time, and the outgoing and incoming edge with given label are ...
Alexander Bowe +3 more
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Making de Bruijn Graphs Eulerian.
, 2022 A directed multigraph is called Eulerian if it has a circuit which uses each edge exactly once. Euler’s theorem tells us that a weakly connected directed multigraph is Eulerian if and only if every node is balanced. Given a collection S of strings over an alphabet Σ, the de Bruijn graph (dBG) of order k of S is a directed multigraph G_{S,k}(V,E), where
G. Bernardini (Giulia) +5 more
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