bruijn graph
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
... de Bruijn graphs for the 62 ...de Bruijn graph for all 62 strains of ...de Bruijn graphs of their first chromosomes (7 × Chr1, con- taining 1736 million base pairs) and the complete seven ...
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A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
... de Bruijn graph constructed from rORFs alone may result in fragmented ...noisy graph using the SVM test dataset (all ORFs translated via six-frame translation) and mapped rORFs to the graph to ...
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Space-efficient and exact de Bruijn graph representation based on a Bloom filter
... de Bruijn graph, which is a de Bruijn graph stored as a Bloom filter (described in the next ...the graph can be encoded with as lit- tle as 4 bits per ...the graph is ...
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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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12859_2018_article_2051.pdf
... de Bruijn graph correction methods (namely seed-and-extend or seed-and-bridge) using the shared ...de Bruijn correction methods require both a k-mer size and frequency thresholds to determine whether ...
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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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Use of regular topology in logical topology design.
... The first row gives the logical node number, and it is always presented in the same order as shown above. The second row shows the physical node number that the logical node is mapped. This example shows that nodeB,D ...
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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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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
... We proposed a novel data structure called the Bloom Fil- ter Trie for storing a pan-genome as a colored de Bruijn graph. The trie stores k-mers and their colors. A new rep- resentation of vertices is ...
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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) if ...
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Framework for Genome Assembly on GPU: A Proposal
... We previously discussed a few algorithms and tool that deal with genome assembly. Even though there are a huge number of serial and parallel assemblers, it still remains the most difficult computation problem in ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... 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 ...the graph topology, and not cover- age, ...
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State of the art de novoassembly of human genomes from massively parallel sequencing data
... Another aspect of human genome short-read assemblers that should be discussed is the genome coverage. As shown with SOAPdenovo, gene cover- age is significantly higher than genome coverage, which indicates that the ...
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The Semifull Graph of a Graph
... planar graph G is the minimum number of points not belonging to the boundary of the exterior region in any embedding of G in the ...A graph G is said to be k-minimally nonouterplanar if i(G) = k, k ≥ ...A ...
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Reproducing the cyclic tag system developed by Matthew Cook with Rule 110 using the phases f1 1
... The evolution space in Figure 4 shows different packages of A gliders, the initial condition is constructed following some of the seven possible cycles of the de Bruijn diagram or a comb[r] ...
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Mathematics in the Age of the Turing Machine - Free Computer, Programming, Mathematics, Technical Books, Lecture Notes and Tutorials
... A formal proof is a proof that has been checked at the level of the primitive rules of inference all the way back to the fundamental axioms of mathematics. The number of primitive inferences is generally so large that it ...
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Case Study on Graph Processing Using Graph Engine
... large graph data has proved of essential importance in the present day ...large graph system, the specific architectural design requirements for different types of data and its application needs in today’s ...
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Survey on Large Graph Analysis and Visualization
... large graph. GMine introduceses the concept of super graph ,Graph tree and CEPS ...sub graph ,it contains collection of paths connecting sub graph of ...query graph nodes and ...
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The Neighborhood Graph of a Graph
... neighborhood graph N(G) of a graph G = (V, E) is the graph with the vertex set V∪S where S is the set of all open neighborhood sets of G and with two vertices u, v ∈ V∪S adjacent if u ∈ V and v is an ...
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Labelings on Jahangir Graph and Extended Duplicate Graph of Jahangir Graph
... a graph G with vertex set V is a function from V(G) to {0,1} such that if each edge uv is assigned the label f(u)f(v), the number of vertices labeled ‘0’ and the number of vertices labeled ‘1’ differ by atmost 1 ...
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