Results 31 to 40 of about 3,685 (173)
RGFA: powerful and convenient handling of assembly graphs [PDF]
PeerJ, 2016 The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA
Giorgio Gonnella, Stefan Kurtz
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Lossless Indexing with Counting de Bruijn Graphs [PDF]
Genome Research, 2021 Abstract Sequencing data is rapidly accumulating in public repositories. Making this resource accessible for interactive analysis at scale requires efficient approaches for its storage and indexing. There have recently been remarkable advances in building compressed representations of annotated
Mikhail Karasikov +3 more
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F1000Research, 2015 The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De ...
Michael R. Crusoe +60 more
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Dynamic construction of pan-genome subgraphs
Open Computer Science, 2020 Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph as a description of a pan-genome, comprising the genomes of many individuals/strains of the same or closely related species. Subsequent work improved the construction of the
Dede Kadir, Ohlebusch Enno
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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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AGORA: Assembly Guided by Optical Restriction Alignment
BMC Bioinformatics, 2012 Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs).
Lin Henry C +6 more
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Properties of the extremal infinite smooth words [PDF]
Discrete Mathematics & Theoretical Computer Science, 2007 Smooth words are connected to the Kolakoski sequence. We construct the maximal and the minimal infinite smooth words, with respect to the lexicographical order.
Srecko Brlek +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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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Genome Biology, 2022 The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck.
Jamshed Khan +3 more
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BMC Bioinformatics, 2017 Background The recent release of the gene-targeted metagenomics assembler Xander has demonstrated that using the trained Hidden Markov Model (HMM) to guide the traversal of de Bruijn graph gives obvious advantage over other assembly methods. Xander, as a
Dinghua Li +5 more
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