GEMmaker

GEMmaker is a Nextflow workflow designed to efficiently quantify gene expression from RNA-seq datasets, ranging from small collections to massive compilations that encompass thousands of samples. It is crafted to meet the growing demands for transcriptome analysis, including differential gene expression analysis and gene co-expression network construction, which have become more complex due to the increasing size and depth of RNA-seq experiments. GEMmaker addresses the challenges associated with managing large datasets, such as data management, computational resource requirements, high-performance computing (HPC) system navigation, software dependencies, and reproducibility.

Key features of GEMmaker include its compliance with nf-core guidelines, ensuring high standards of practice, and its use of versioned, containerized software, which enhances reproducibility across various computing environments—from individual workstations to cloud platforms. This flexibility is particularly beneficial for users with varying access levels to computational resources. GEMmaker supports popular RNA-seq alignment and quantification tools and provides results in both raw and normalized formats. Its unique capability to handle thousands of samples, whether stored locally or remotely, without overwhelming data storage capacities sets it apart from existing gene expression quantification workflows.