RASflow

RASflow implements a Snakemake-based RNA-Seq analysis workflow for preprocessing reads, aligning them to genomic or transcriptomic assemblies, and quantifying gene and transcript expression.

Key Features:

• Modular and Flexible Design: Uses Snakemake as the workflow management system to provide a modular structure that permits customization of analysis pipelines.
• Conda-based Dependency Management: Uses Conda for package management and dependency resolution to support reproducible software environments.
• Support for Genomic and Transcriptomic Assemblies: Supports alignment to both genomic and transcriptomic reference assemblies.
• Read Preprocessing: Performs preprocessing of RNA-Seq reads.
• Read Alignment: Aligns reads to reference assemblies.
• Expression Quantification: Quantifies gene and transcript expression levels across samples.
• Reproducibility: Ensures reproducibility through Snakemake workflow execution and Conda-managed environments.

Scientific Applications:

• Gene Expression Quantification: Enables quantification of gene and transcript expression from RNA-Seq data.
• Regulatory and Expression Pattern Studies: Supports analyses aimed at investigating gene regulation and expression patterns, including complex regulatory studies.
• Analyses Across Model and Non-model Organisms: Applicable to studies using model organisms and non-model species via support for genomic or transcriptomic assemblies.

Methodology:

Preprocessing of RNA-Seq reads, alignment to genomic or transcriptomic reference assemblies, and quantification of gene or transcript expression levels across samples; Snakemake orchestrates workflow execution and Conda manages software dependencies.