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ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

McLaughlin, R. J.; Chen, S.; Nag, A.; Noonan, A. J. C.; Bartolomeu, C.; Borden, S. A.; Lam, S.; Myers, R.; Hallam, S. J.

2026-08-11 bioinformatics
10.64898/2026.08.05.743000 bioRxiv
Show abstract

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, an accessible Nextflow workflow for processing, analyzing, and interpreting linked ASV-VOC data from respiratory microbiome studies. 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 implementationThe ASPIRE workflow, quick start guide, and usage are freely available on the GitHub platform https://github.com/hallamlab/ASPIRE. ASPIRE is implemented in Nextflow with a modular design to allow for reproducibility, extensibility and scalability.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.