Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a “QC-Preprocess-QC” workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster.We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.

As the key component of intravascular ultrasound (IVUS) imaging systems, traditional commercial side-looking IVUS transducers are flat and unfocused, which limits their lateral resolution. We propose a PMN-PT single crystal IVUS transducer with a half-concave geometry. This unique configuration makes it possible to conduct geometric focusing at a desired depth. To compare performances, the proposed and the traditional flat transducer with similar dimensions were fabricated. We determined that the half-concave transducer has a slightly higher center frequency (35 MHz), significantly broader -6 dB bandwidth (54%) but a higher insertion loss (-22.4 dB) compared to the flat transducer (32 MHz, 28%, and -19.3 dB, respectively). A significant enhancement of the lateral resolution was also confirmed. The experimental results are in agreement with the finite element simulation results. This preliminary investigation suggests that the half-concave geometry design is a promising approach in the development of focused IVUS transducers with broad bandwidth and high lateral resolution.

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