SOAPnuke

SOAPnuke performs integrated quality control and preprocessing of high-throughput sequencing data to prepare reads for downstream analysis.

Key Features:

• Integrated QC-Preprocess-QC Workflow: Integrates initial quality control, preprocessing, and a second round of QC in a single executable framework to avoid file reformatting between steps.
• Modular Design: Provides four modules tailored for genomic sequencing, small RNA analysis, Digital Gene Expression (DGE), and metagenomics.
• MapReduce Acceleration Framework: Leverages the MapReduce framework to distribute processing across compute clusters for scalable parallel execution.
• Scalability and Performance: On a ~30× NA12878 dataset from the Genome in a Bottle Consortium (GIAB), achieved approximately 5.7× faster processing on 16 nodes while maintaining a balance between resource occupancy and performance.

Scientific Applications:

• Genomic sequencing: Preprocessing and QC for whole-genome and targeted genomic sequencing datasets.
• Small RNA analysis: Quality control and preprocessing tailored for small RNA sequencing experiments.
• Digital Gene Expression (DGE): Preprocessing and QC for DGE profiling workflows.
• Metagenomics: Preprocessing and QC for metagenomic sequencing datasets.

Methodology:

Implements a "QC-Preprocess-QC" workflow performing initial quality checks, preprocessing tailored to sequencing data type, and post-processing QC, and uses the MapReduce framework for distributed parallel processing.