MHASS: Microbiome HiFi Amplicon Sequencing Simulator
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arXiv
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| Format: | Preprint |
| Published: |
2025
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| _version_ | 1866916950856171520 |
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| author | Howard-Stone, Rye Mandoiu, Ion |
| author_facet | Howard-Stone, Rye Mandoiu, Ion |
| contents | 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.
Contact: rye.howard-stone@uconn.edu or ion.mandoiu@uconn.edu
Supplementary information: Supplementary data are available online at https://github.com/rhowardstone/MHASS_evaluation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_12428 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | MHASS: Microbiome HiFi Amplicon Sequencing Simulator Howard-Stone, Rye Mandoiu, Ion Genomics 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. Contact: rye.howard-stone@uconn.edu or ion.mandoiu@uconn.edu Supplementary information: Supplementary data are available online at https://github.com/rhowardstone/MHASS_evaluation. |
| title | MHASS: Microbiome HiFi Amplicon Sequencing Simulator |
| topic | Genomics |
| url | https://arxiv.org/abs/2509.12428 |