STAR Suite: Integrating transcriptomics through AI software engineering in the NIH MorPhiC consortium

To accommodate rapid methodological turnover, bioinformatics pipelines typically consist of discrete binaries linked via scripts. While flexible, this architecture relies on intermediate files, sacrificing performance, and treating complex codebases as static silos. For example, the STAR aligner [1]-the standard engine for transcriptomics-uses an external script for adapter trimming, necessitating the decompression and re-compression of large files. These limitations presented scalability problems for uniform processing of data in the NIH MorPhiC consortium. We present our solution, STAR Suite, a human-engineered and AI-implemented modernization that integrates functionality directly into the C++ source. In just four months, a single developer added over 92,000 lines to the original 28,000-line codebase to produce four unified modules: STAR-core, STAR-Flex, STAR-Perturb, and STAR-SLAM that can be installed as a pre-compiled binary without introducing any new dependencies. This work demonstrates a new paradigm for the rapid evolution of high-performance bioinformatics software.