AutoRNAseq: Automated Bulk RNA-seq Analysis Pipeline

Improved accessibility of high-throughput RNA sequencing has increased the amount of data generated each year. This increase in data creates a need for reproducible pipelines that can process RNA-seq data consistently across experiments. AutoRNAseq addresses this need by providing a Snakemake-based workflow for bulk RNA-seq analysis by automating data retrieval, quality control, and gene quantification. Unlike existing RNA-seq workflows that require users to coordinate multiple pipelines and pre-configure reference data, AutoRNAseq provides a single, end-to-end workflow that automates data acquisition, reference preparation, quality control, alignment, and quantification with minimal user intervention. AutoRNAseq is applicable to any domain requiring consistently processed RNA-seq datasets, including bioinformatics, computational biology, and drug-response studies.