The STAR aligner plays a key role in complex transcriptomics pipelines consisting of multiple analytical tools. We present STAR Suite, a drop-in replacement for STAR that internalizes entire pipelines for bulk RNA-seq, scRNA-seq, Perturb-seq, 10x Flex, and SLAM-seq. Deployed by the NIH MorPhiC consortium, STAR Suite provides an open-source alternative to proprietary Cell Ranger pipelines, achieving gene-level Pearson correlations of 0.99-1.0 and 3.8- to 5.7-fold faster speeds for Perturb-seq and Flex analysis through improved methodologies. Integrating multi-module workflows into a single executable makes STAR Suite ready-to-use for both human researchers and the AI agents increasingly used in analytical workflows. STAR Suite was developed using AI agents, enabling a single developer to add 97,000 lines of code to the 28,000-line codebase in four months--illustrating a modern paradigm for large-scale integration of complex open-source codebases by individual research groups. Utilities are included to facilitate future community contributions using AI assistants.
Hung, L.-H. et al. · CC-BY 4.0