Results 11 to 20 of about 131,326 (303)
Metagenomic binning with assembly graph embeddings [PDF]
Bioinformatics, 2022 Abstract Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have
Andre Lamurias +4 more
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Faucet: streaming de novo assembly graph construction. [PDF]
Bioinformatics, 2018 Motivation We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed.
Rozov R +3 more
europepmc +2 more sources
Assembly Graph as the Rosetta Stone of Ecological Assembly [PDF]
Environmental MicrobiologyABSTRACT Ecological assembly—the process of ecological community formation through species introductions—has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non‐theoreticians, and they lack a unifying lens.
Song, Chuliang
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GTasm: a genome assembly method using graph transformers and HiFi reads [PDF]
Frontiers in GeneticsMotivationGenome assembly aims to reconstruct the whole chromosome-scale genome sequence. Obtaining accurate and complete chromosome-scale genome sequence serve as an indispensable foundation for downstream genomics analyses.
Junwei Luo +4 more
doaj +3 more sources
Modified Classical Graph Algorithms for the DNA Fragment Assembly Problem [PDF]
Algorithms, 2015 DNA fragment assembly represents an important challenge to the development of efficient and practical algorithms due to the large number of elements to be assembled.
Guillermo M. Mallén-Fullerton +3 more
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Flowtigs: Safety in flow decompositions for assembly graphs
iScience, 2023 Summary: A decomposition of a network flow is a set of weighted walks whose superposition equals the flow. In this article, we give a simple and linear-time-verifiable complete characterization (flowtigs) of walks that are safe in such general flow ...
Francisco Sena +5 more
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Assembly Graph Browser: interactive visualization of assembly graphs [PDF]
Bioinformatics, 2019 Abstract Summary Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser
Alla Mikheenko, Mikhail Kolmogorov
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The Number of Ways to Assemble a Graph [PDF]
2013 Proceedings of the Tenth Workshop on Analytic Algorithmics and Combinatorics (ANALCO), 2012 Motivated by the question of how macromolecules assemble,the notion of an assembly tree of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies to the macromolecular assembly problem. Explicit formulas or generating functions are provided for the number of assembly
Andrew Vince, Miklós Bóna
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Robust Self-assembly of Graphs [PDF]
Natural Computing, 2009 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Stanislav Angelov +2 more
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AND/OR graph representation of assembly plans [PDF]
IEEE Transactions on Robotics and Automation, 1990 Robotics ...
Luiz Homem de Mello, Arthur C. Sanderson
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