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pmid:41351823

MHASS: Microbiome HiFi Amplicon Sequencing Simulator.

Rye Howard-Stone · Ion I Măndoiu

Bioinformatics (Oxford, England) · 2026 doi:10.1093/bioinformatics/btaf656

Paper

complete

Experiment

partial

Data

partial

Analysis

complete

Execution

absent

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MHASS: Microbiome HiFi Amplicon Sequencing Simulator.
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Rye Howard-Stone
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Ion I Măndoiu
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abstract
SUMMARY: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies, and empirically derived pass-number distributions from actual sequencing runs. MHASS generates datasets tailored for rigorous benchmarking and validation of long-read microbiome analysis workflows, including ASV clustering and taxonomic assignment. AVAILABILITY AND IMPLEMENTATION: Implemented in Python with automated dependency management, the source code for MHASS is freely available at https://github.com/rhowardstone/MHASS along with installation instructions. Our code is also published on Zenodo at https://doi.org/10.5281/zenodo.17486364. The data underlying this article are available on GitHub at https://github.com/rhowardstone/MHASS_evaluation/.
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ASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrat
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