Results 31 to 40 of about 2,351 (162)
A family of tree-based generators for bubbles in directed graphs
Journal of Graph Algorithms and Applications, 2021 Bubbles are pairs of internally vertex-disjoint $(s, t)$-paths in a directed graph. In de Bruijn graphs built from reads of RNA and DNA data, bubbles represent interesting biological events, such as alternative splicing (AS) and allelic differences (SNPs
Vicente Acuña +5 more
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Comparing methods for constructing and representing human pangenome graphs
Genome Biology, 2023 Background As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses.
Francesco Andreace +3 more
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Hybrid-hybrid correction of errors in long reads with HERO
Genome Biology, 2023 Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO,
Xiongbin Kang +3 more
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Discrete Mathematics, 1991 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Roy D. Bryant, Harold Fredricksen
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Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ
Nature Communications, 2020 Multiple whole-genome alignment is a challenging problem in bioinformatics, especially when computational resources are limited. Here the authors present SibeliaZ, an algorithm and software based on analysis of de Bruijn graphs, which provides improved ...
Ilia Minkin, Paul Medvedev
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Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers [PDF]
Journal of Computational Biology, 2011 Mark Chaisson +2 more
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Pan-genome de Bruijn graph using the bidirectional FM-index
BMC Bioinformatics, 2023 Background Pan-genome graphs are gaining importance in the field of bioinformatics as data structures to represent and jointly analyze multiple genomes. Compacted de Bruijn graphs are inherently suited for this purpose, as their graph topology naturally ...
Lore Depuydt +3 more
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TahcoRoll: fast genomic signature profiling via thinned automaton and rolling hash
Medical Review, 2021 Genomic signatures like k-mers have become one of the most prominent approaches to describe genomic data. As a result, myriad real-world applications, such as the construction of de Bruijn graphs in genome assembly, have been benefited by recognizing ...
Ju Chelsea J.-T. +4 more
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Assembly complexity of prokaryotic genomes using short reads
BMC Bioinformatics, 2010 Background De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads.
Pop Mihai +2 more
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Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
BMC Bioinformatics, 2010 Background Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they ...
Vaughn Matthew +4 more
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