Where Signal Meets Structure
Open-source single-molecule long-read sequencing software and research from the Athey Lab at the University of Michigan — Oxford Nanopore and PacBio HiFi methods for pharmacogenomics, targeted enrichment, and single-molecule error characterization.
Lab Pulse
Research Themes
Pharmacogenomics
Long-read sequencing of pharmacogenomic loci — including the complex CYP2D6 region — with haplotype-aware star-allele calling and clinical-actionability reporting.
Learn more →Targeted Enrichment
Cas9/CRISPR-based targeted sequencing and real-time nanopore adaptive sampling for focused, cost-efficient long-read panels.
Learn more →Single-Molecule Accuracy
Empirical characterization of per-read error rates and basecaller behavior using sequence-defined DNA standards and reference-grade controls.
Learn more →Long-Read Bioinformatics
End-to-end pipelines for Oxford Nanopore and PacBio HiFi data — basecalling, alignment, methylation handling, structural-variant calling, and visualization.
Learn more →Assay Development
Wet-lab methods for guide-panel design, nickase chemistry, library-prep optimization, and fragment-analysis QC.
Learn more →Statistical Methods
Bayesian and likelihood-based inference for haplotype classification, assay-efficiency modeling, and single-molecule confidence quantification.
Learn more →Open Software
ONT-SMA-seq
Single-Molecule Accuracy sequencing workflow for Oxford Nanopore — pure Python plus SQLite for reproducible per-read error measurement.
Repo →CypScope
Read-coverage and QC reporting across the CYP2D6, CYP2D7, and CYP2D8P region for ONT sequencing data.
Repo →barbell
Fast and accurate nanopore demultiplexing — implemented in Rust for high-throughput barcode assignment.
Repo →dorado-run
Oxford Nanopore Dorado basecaller orchestration pipeline — reproducible batch runs and model management.
Repo →fragment-viewer
Interactive CE / GeneMapper fragment analyzer. Electropherograms, dye-calibrated peak classification, Cas9 cut-site prediction.
Open viewer →PGx-prep
Preparatory demultiplexing and HPC/SLURM workflows on BAM files for the ONT pharmacogenomics pipeline.
Repo →Public Resources
ont-ecosystem
Public documentation for the lab's Oxford Nanopore analysis framework — library modules, CLI tools, and reusable analysis skills.
Docs →Knowledge Graph
Lab knowledge snapshot
Weekly snapshot of the lab's ambient knowledge graph built from papers, decisions, transcripts, experiments, and registries. Snapshot of 2026-04-24: 2547 entities, 24236 entity mentions across 26354 sources; 50 new entities in the last 7 days.
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