K-mer Mapping and de Bruijn graphs: The case for velvet fragment assembly

Armas, Elvismary Molina de; Hæusler, Edward Hermann; Lifschitz, Sérgio; Holanda, Maristela; Silva, Waldeyr Mendes Cordeiro da; Ferreira, Paulo Cavalcanti Gomes

doi:10.1109/bibm.2016.7822642

Cited by 5 publications

(1 citation statement)

References 23 publications

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“…e velvet algorithm is verified on simulation data and real data, and the maximum N50 can reach 50k. In recent years, there have been many applications and research studies on the velvet algorithm [28]. e main steps of the velvet algorithm are as follows:…”

Section: Domain Analysismentioning

confidence: 99%

Gene Sequence Assembly Algorithm Model Based on the DBG Strategy and Its Application

Shi

2021

Journal of Healthcare Engineering

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With the continuous development of sequencing technology, the amount of bioinformatics data has increased geometrically, and the massive amount of bioinformatics data puts forward more stringent requirements for sequence assembly problems. The sequence assembly algorithm based on DBG (De Bruijn graph) strategy is a key algorithm in bioinformatics, which is widely used in the domain of gene sequence assembly. Current research on the domain of sequence assembly always focuses on optimization of specific steps to a specific algorithm and lack of research on domain-level high-abstract algorithm frameworks. To some extent, it leads to the redundancy of the sequence assembly algorithm, and some problems may be caused by the artificial selection algorithm. This paper analyzes the domain of DBGSA and establishes a feature model of this domain. Based on the production programming method, the DBGSA algorithm component is interactively designed. With the support of the PAR platform, the DBGSA algorithm component library is formally implemented, and furthermore, the DBGSA component library is used to assemble the specific algorithm. This research adds domain-level research to the domain of sequence assembly and implements the DBGSA component library, which can assemble specific sequence assembly algorithms, ensuring the efficiency of algorithm development and the reliability of assembly generation algorithms. At the same time, it also provides a valuable reference for solving problems in the domain of sequence assembly.

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Section: Domain Analysismentioning

confidence: 99%