End-to-end bulk RNA-seq Quantification Pipeline using Salmon

Overview

This repository contains a publication-ready RNA-seq quantification pipeline built around Salmon for lightweight and accurate transcript quantification.
It automates the full workflow from SRA download ? FASTQ generation ? Transcript quantification (Salmon), followed by R-based downstream analysis (DESeq2, functional enrichment, and visualization). The pipeline is designed for reproducibility, modularity, and high-performance computing environments, with detailed timing logs for benchmarking.

Features

• Fully automated and parallelized
• Ready for downstream DESeq2 analysis in R
• Conda-based reproducible environment via environment.yml
• Organized directory structure for clarity and reproducibility

Create a directory to store your references

mkdir -p ~/references/hg38 cd ~/references/hg38

Quick Start

conda env create -f environment.yml
conda activate salmon-rnaseq