CoRRDe Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in modern computers.
Daniel Górniak, Robert Nowak 0002
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De Bruijn Graph Homomorphisms and Recursive De Bruijn Sequences
CoRR, 2008 This paper presents a method to find new De Bruijn cycles based on ones of lesser order. This is done by mapping a De Bruijn cycle to several vertex disjoint cycles in a De Bruijn digraph of higher order and connecting these cycles into one full cycle.
Abbas Alhakim, Mufutau Akinwande
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De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
BMC Bioinformatics, 2018 Background Many organisms, in particular bacteria, contain repetitive DNA fragments called tandem repeats. These structures are restored by DNA assemblers by mapping paired-end tags to unitigs, estimating the distance between them and filling the gap ...
Wiktor Kuśmirek, Robert Nowak
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CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq. [PDF]
Brief Bioinform, 2023 Wang Y +5 more
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MBG: Minimizer-based sparse de Bruijn Graph construction. [PDF]
Bioinformatics, 2021 Rautiainen M, Marschall T.
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Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph. [PDF]
Algorithms Mol Biol, 2021 Mukherjee K +3 more
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Integrative Comparison of Burrows-Wheeler Transform-Based Mapping Algorithm with de Bruijn Graph for Identification of Lung/Liver Cancer-Specific Gene. [PDF]
J Microbiol Biotechnol, 2022 Ajaykumar A, Yang JJ.
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A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes. [PDF]
BMC Bioinformatics, 2021 Guo J, Pang E, Song H, Lin K.
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An extended de Bruijn graph for feature engineering over biological sequential data
Machine Learning: Science and TechnologyIn this study, we introduce a novel de Bruijn graph (dBG) based framework for feature engineering in biological sequential data such as proteins. This framework simplifies feature extraction by dynamically generating high-quality, interpretable features ...
Mert Onur Cakiroglu +6 more
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