SPEAQeasy

SPEAQeasy performs end-to-end processing of RNA sequencing (RNA-seq) data to produce quality-controlled reads, alignments, quantified counts, and inputs for differential gene expression and Bioconductor-based downstream analysis.

Key Features:

• Comprehensive workflow: Processes raw RNA-seq FASTQ files through quality control, alignment, quantification, and differential gene expression preparation in a single pipeline.
• Analytical steps: Includes explicit stages for quality control, alignment, quantification, and differential expression analysis.
• Workflow orchestration: Implemented using Nextflow for pipeline management.
• Containerization: Supports Docker containerization for software environment consistency.
• Resource manager compatibility: Compatible with SLURM and SGE resource managers for scalable execution.
• Reproducibility and configuration: Uses configuration files to accommodate different computational setups and promote consistent results.
• Modularity: Designed as a modular pipeline allowing customization of specific processing steps.
• Integration with R/Bioconductor: Produces outputs formatted for downstream analysis with R and Bioconductor tools.

Scientific Applications:

• Differential gene expression studies: Generates quantified counts and inputs suitable for differential expression analysis.
• RNA-seq data processing: Provides end-to-end preprocessing and quantification of RNA-seq datasets from FASTQ reads.
• Downstream statistical analysis and visualization: Supplies outputs compatible with R/Bioconductor for statistical testing and visualization of biological processes and disease mechanisms.

Methodology:

Processes raw RNA-seq reads through quality control, alignment, quantification, and differential expression analysis; implemented in Nextflow with Docker support, compatible with SLURM and SGE, and configurable via pipeline configuration files in a modular design.