de Bruijn graph
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
... compressed de Bruijn graphs for the 62 ...compressed de Bruijn ...compressed de Bruijn graph for all 62 strains of ...compressed de Bruijn graphs of their ...
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Space-efficient and exact de Bruijn graph representation based on a Bloom filter
... probabilistic de Bruijn graph. (a) shows S , an example de Bruijn graph (the 7 non-dashed nodes), and B , its probabilistic representation from a Bloom filter (taking the union ...
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A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
... traditional graph, indicating that sequencing errors and false frame trans- lations increased the complexity of the codon-based de Bruijn ...codon-based de Bruijn graph, the gene ...
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deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph based index
... Conclusion Overall, the benchmark results on simulated and real datasets demonstrate that the two-pass approach of deSALT is suited to address several difficult technical issues in long [r] ...
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Using cascading Bloom filters to improve the memory usage for de Brujin graphs
... The key idea of [9] is to explicitly store only a small sub- set of all false positives of B, the so-called critical false positives. Consider a k-mer u that belongs to T, u has at most 2 || = 8 potential neighbors, i.e. ...
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Jabba: hybrid error correction for long sequencing reads
... Background: Third generation sequencing platforms produce longer reads with higher error rates than second generation technologies. While the improved read length can provide useful information for downstream analysis, ...
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Konnector v2.0: pseudo-long reads from paired-end sequencing data
... filter de Bruijn graph is constructed by shredding the input reads into k-mers, and loading the k-mers into a Bloom ...the de Bruijn graph, are stored in the Bloom filter whereas ...
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole Genome Sequences
... (de Bruijn graph based) and Genefinder (or equiva- lent mapping-based program such as SRST2 [22]) are a sensible combination to use as an initial consensus method, followed by Typewriter (BLAST based) ...
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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
... labeled de Bruijn graph with it requires concatenated raw sequence files as input, where it is not possible to specify a minimum number of occurences per ...
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Use of regular topology in logical topology design.
... The other function used for the evaluation is the fitness function. The objective of the proposed genetic algorithm is to find a mapping between the physical nodes of the network and the logical nodes of the scalable ...
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Fast read alignment with incorporation of known genomic variants
... In order to achieve a lower RAM usage during our dynamically construction of pseudo-tree based struc- ture variation tree with different genomic sequence and regional indeded varians in the process of seed extension, we ...
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12859_2018_article_2051.pdf
... effective de novo assembly with less long read data than previously ...a de Bruijn graph that support multiple values of k [27, ...efficient de novo assembly ...
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State of the art de novoassembly of human genomes from massively parallel sequencing data
... the de Bruijn graph step, neither ABySS nor SOAPdenovo take advan- tage of paired-end information in the initial contig ...original de Bruijn graph could be explained by ...
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Framework for Genome Assembly on GPU: A Proposal
... the de Bruijn graph. The graph construction runs using the command Velvetg as shown in figure ...velvet de novo assembler builds a sequence of the genome by a traversal done to the ...
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TransLiG: a de novo transcriptome assembler that uses line graph iteration
... of de novo assem- blers, such as BinPacker [23], Bridger [24], Trinity [12], IDBA-Tran [25], SOAPdenovo-trans [26], ABySS [27], and Oases ...the de novo assembly of tran- ...a de bruijn ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... the de Bruijn Graph. Within these complex parts of the graph generated by repeats, any assembler will have to choose the “right” path(s) among the many ...for de novo transcriptome ...
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Lp Inequalities for Polynomials
... to De-Bruijn [9] for p 1 and Rahman and Schmeisser [10] extended it for 0 < p < 1 whereas the Inequality (6) was proved by Boas and Rahman [11] for p 1 and later it was extended for 0 < p < ...
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On complexity of chaotic elementary cellular automaton with memory: Rule 126
... Coding gliders by basin representation Coding gliders since de Bruijn diagrams Implementing basic functions.. Conclusions Final remarks..[r] ...
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In gesprek met J.R. Bruijn
... stond de voeding aan boord van oorlogsschepen centraal. Hoe werd dat georganiseerd en gefinancierd - dat vond ik interessant. De voeding bleek de belangrijkste bron van inkomsten voor e[r] ...
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The Semifull Graph of a Graph
... other graph valued functions in graph theory were studied, for example, in [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,41] and also graph valued functions in domination theory were studied, for ...
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