ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

Summary: Microbial communities inhabiting the respiratory tract contribute to health status through interactions with host physiology, immune function, and local environmental conditions. Advances in small subunit ribosomal RNA (SSU or 16S rRNA) gene amplicon sequencing enable culture-independent profiling of microbial communities as amplicon sequence variants (ASVs), revealing links between microbial dysbiosis and respiratory diseases, and the use of mass spectrometry to measure volatile organic compounds (VOCs) in exhaled breath shows emerging promise for biomarker discovery. Here we present ASPIRE, the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems, for processing, analyzing, and interpreting linked ASV-VOC data from respiratory microbiome studies and beyond. ASPIRE is designed to support scalable comparative analysis across respiratory sample types while preserving intermediate file outputs for inspection and reuse within a standardized file structure. Availability and implementation: The complete workflow, test data, and required documentation are publicly available as a GitHub repository at https://github.com/hallamlab/ASPIRE. ASPIRE is implemented in Nextflow with a modular design architecture for reproducibility, extensibility and scalability.