Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields [PDF]
BMC Bioinformatics, 2020 Background De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence.
Aranka Steyaert +2 more
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Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs [PDF]
BMC Bioinformatics, 2023 Background Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes.
Lisa Fiedler +3 more
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Succinct colored de Bruijn graphs. [PDF]
Bioinformatics, 2017 Abstract Iqbal et al. (Nature Genetics, 2012) introduced the colored de Bruijn graph , a variant of the classic de Bruijn graph, which is aimed at “detecting and genotyping simple and complex genetic variants in an individual or population”.
Muggli MD +8 more
europepmc +4 more sources
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs [PDF]
BMC Bioinformatics, 2017 Background The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other assembly methods. Xander, as a
Dinghua Li +5 more
doaj +2 more sources
Read mapping on de Bruijn graphs. [PDF]
BMC Bioinformatics, 2016 Abstract Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig describes the sequence found along some path of the assembly graph, however, the
Limasset A +3 more
europepmc +7 more sources
BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs [PDF]
PeerJ, 2018 Dramatic increases in data produced by next-generation sequencing (NGS) technologies demand data compression tools for saving storage space. However, effective and efficient data compression for genome sequencing data has remained an unresolved challenge
Rongjie Wang +4 more
doaj +3 more sources
De Bruijn sequences and De Bruijn graphs for a general language
Information Processing Letters, 2005 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Eduardo Moreno
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Cycle Structure and Adjacency Graphs of a Class of LFSRs and a New Family of De Bruijn Cycles
IEEE Access, 2018 Feedback shift registers can be applied to the fields of communications, stream ciphers, computers, and design theory. The linear feedback shift registers are often used in the construction of De Bruijn sequences. For any given linear shift register, its
Linzhi Jiang, Xiaofang Wang
exaly +3 more sources
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs [PDF]
BMC Bioinformatics, 2018 Background Aligning short reads to a reference genome is an important task in many genome analysis pipelines. This task is computationally more complex when the reference genome is provided in the form of a de Bruijn graph instead of a linear sequence ...
Mahdi Heydari +3 more
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The Collatz conjecture and De Bruijn graphs
Indagationes Mathematicae, 2013 9 pages, 8 ...
Thijs Laarhoven
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