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Counting is the type of measurement that is free from uncertainty, provided the number of objects being counted does not change during the process. Such measurements result in exact numbers. By counting the eggs in a carton, for instance, one can determine exactly how many eggs are there in the carton. Similarly, the numbers of defined quantities are also exact. For example, 1 foot is exactly 12 inches, 1 inch is exactly 2.54 centimeters, and 1 gram is exactly 0.001 kilograms. Quantities...
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The Fast Fourier Transform (FFT) is a computational algorithm designed to compute the Discrete Fourier Transform (DFT) efficiently. By breaking down the calculations into smaller, manageable sections, the FFT significantly reduces the computational complexity involved. Direct computation of an N-point DFT requires N2 complex multiplications, whereas the FFT algorithm needs only (N/2)log⁡2N multiplications, offering a much faster performance.
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Determining the subtransient fault current in a power system involves representing transformers by their leakage reactances, transmission lines by their equivalent series reactances, and synchronous machines as constant voltage sources behind their subtransient reactances. In this analysis, certain elements are excluded, such as winding resistances, series resistances, shunt admittances, delta-Y phase shifts, armature resistance, saturation, saliency, non-rotating impedance loads, and small...
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Related Experiment Video

Updated: Feb 4, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

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Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach.

Arash Bayat, Nandan P Deshpande, Marc R Wilkins

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |October 12, 2018
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    Summary

    We adapted a fast long-read genome assembly method for short reads, creating MiniSR. This new pipeline offers a good balance between speed and accuracy for bacterial and small eukaryotic genomes.

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Computational Biology

    Background:

    • De novo genome assembly is computationally intensive.
    • Long-read sequencing has introduced novel assembly algorithms.
    • Existing short-read assemblers present speed-accuracy trade-offs.

    Purpose of the Study:

    • To adapt a long-read assembly technique for short-read genome assembly.
    • To develop a de novo assembly pipeline (MiniSR) balancing speed, accuracy, and contiguity.
    • To evaluate MiniSR against existing short-read assembly tools.

    Main Methods:

    • Modification of a long-read assembly approach (Minimap2 and Miniasm) for short reads.
    • Development of the MiniSR pipeline.
    • Comparative analysis of MiniSR with Spades, SGA, and SOAPdenovo2 using bacterial and small eukaryotic genomes.

    Main Results:

    • MiniSR demonstrates significant speed improvements over Spades (6x) and SGA (2.2x).
    • MiniSR achieves superior contiguity (N50, NGA50) compared to SGA.
    • MiniSR offers a balanced trade-off between assembly speed, accuracy, and contiguity, though Spades yields more complete assemblies.

    Conclusions:

    • The MiniSR pipeline provides an efficient and balanced approach for de novo short-read genome assembly.
    • MiniSR presents a competitive alternative to existing tools, particularly when speed and contiguity are prioritized.
    • The study highlights the potential of adapting long-read strategies for short-read assembly challenges.