SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
By Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li and 5 more. GigaScience, 2017
1,927 citations recorded by the source corpus.
Abstract 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.
Subfields: Ecology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/f99bbfbc5c7bae142cbcd8bec4d5ada5c0578313
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Citations in the corpus
- fastp: an ultra-fast all-in-one FASTQ preprocessor (2018, methodology): “SOAPnuke (Y. Chen et al., 2018) is a recently published tool for adapter trimming and read filtering with the implementation of MapReduce on Hadoop systems.”