ASPIRE: Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

Build amplicon sequence variants (ASVs), assign taxonomy, screen non-targets and contaminants, and connect microbial community profiles to sample metadata, Volatile Organic Compounds (VOCs) and genome references.

Start here: install ASPIRE, then run the public workflow test. The launcher manages Mamba environments and Nextflow. Use the study walkthrough when you are ready to analyze your own samples.

SVG · PDF · Workflow details and diagrams

Arrows trace the main data path. Control decontamination precedes biological feature filtering and metadata construction. Optional analyses depend on configuration.

Getting started

• Installation
• Quickstart and installation test
• Larger demonstration: aspire-cami-mock
• Run your own study
• Inputs and references

Run and understand analyses

• Workflow, architecture and data flow
• Primer removal before fastp
• Decontamination and non-target filtering
• Choose and interpret analyses
• Outputs and run review
• VOC analysis: exploratory displays and patient-level inference

Configuration and advanced use

• ASPIRE Configuration Reference
• Complete ASPIRE Configuration Parameter Catalogue
• ASPIRE Process and I/O Reference
• ASPIRE Expert Guide
• Troubleshooting
• SPARK and ASPIRE manuscript functionality
• Maintain and publish the documentation

Source code · Issues and feature requests

Cite ASPIRE

If you use ASPIRE, please cite:

McLaughlin, R. J., Chen, S., Nag, A., Noonan, A. J. C., Bartolomeu, C., Borden, S. A., Lam, S., Myers, R., & Hallam, S. J. (2026). ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems. bioRxiv, version 2 (12 August 2026). DOI: 10.64898/2026.08.05.743000 · Read version 2.