SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

TLDR

Quality control and preprocessing are essential for sequencing data analysis, yet existing tools lack integrated functions, robust architecture, and scalable acceleration. This study introduces SOAPnuke, a comprehensive QC‑preprocess‑QC workflow that incorporates a MapReduce acceleration framework. SOAPnuke comprises four modules for genomic, small RNA, DGE, and metagenomic data, centralizes processing into a single executable, and distributes work across a compute cluster via MapReduce, as demonstrated in a benchmark on a ∼30× NA12878 dataset. In standalone mode, SOAPnuke balances resource usage and performance, and when run on 16 nodes with MapReduce it achieves approximately 5.7‑fold speedup over competing tools.

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.