Robust data storage in DNA by de Bruijn graph-based de novo strand assembly [PDF]
Nature Communications, 2022 DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. Here the authors present a strand assembly algorithm (DBGPS) using de Bruijn graph and greedy path search.
Lifu Song +11 more
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Pan-genome de Bruijn graph using the bidirectional FM-index [PDF]
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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HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly [PDF]
International Journal of Genomics, 2017 Background. The rapid advancement of sequencing technologies has made it possible to regularly produce millions of high-quality reads from the DNA samples in the sequencing laboratories. To this end, the de Bruijn graph is a popular data structure in the
Md Mahfuzer Rahman +3 more
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Evaluating de Bruijn graph assemblers on 454 transcriptomic data. [PDF]
PLoS ONE, 2012 Next generation sequencing (NGS) technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets ...
Xianwen Ren +6 more
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Detecting circular RNA from high-throughput sequence data with de Bruijn graph [PDF]
BMC Genomics, 2020 Background Circular RNA is a type of non-coding RNA, which has a circular structure. Many circular RNAs are stable and contain exons, but are not translated into proteins.
Xin Li, Yufeng Wu
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Compression algorithm for colored de Bruijn graphs
Algorithms for Molecular Biology, 2023 A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search ...
Amatur Rahman +2 more
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A reinforcement learning approach to effective forecasting of pediatric hypoglycemia in diabetes I patients using an extended de Bruijn graph [PDF]
Scientific ReportsPediatric diabetes I is an endemic and an especially difficult disease; indeed, at this point, there does not exist a cure, but only careful management that relies on anticipating hypoglycemia.
Mert Onur Cakiroglu +5 more
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Looking for a Straw in a Haystack by Bridging the Cracks Between Individual Judgments: Narrowing the Knowledge Gap To Anticipate Surprises by Transforming Risk Assessors' Small Worlds Into Large Worlds. [PDF]
Risk AnalABSTRACT The world is constantly changing, yet a risk assessment is based on the knowledge available at one point in time. There will therefore be a gap between the range of possibilities known or conceivable to the assessor at that time and all the possibilities that could occur over infinite time.
Derbyshire J, Aven T.
europepmc +2 more sources
Sama: a contig assembler with correctness guarantee [PDF]
Algorithms for Molecular BiologyBackground: In genome assembly the task is to reconstruct a genome based on sequencing reads. Current practical methods are based on heuristics which are hard to analyse and thus such analysis is not readily available.
Leena Salmela
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KSNP: a fast de Bruijn graph-based haplotyping tool approaching data-in time cost [PDF]
Nature CommunicationsLong reads that cover more variants per read raise opportunities for accurate haplotype construction, whereas the genotype errors of single nucleotide polymorphisms pose great computational challenges for haplotyping tools.
Qian Zhou +5 more
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