bioconda/bioconda-recipes
May 2026 – May 2026
1 Month active
Languages Used
Python
Technical Skills
BioinformaticsCLI DevelopmentData Analysis
Greg Farnum
PROFILE
Greg Farnum
Developed a comprehensive command-line tool for Oxford Nanopore end_reason metadata analysis, integrated within the bioconda/bioconda-recipes repository. The project focused on bioinformatics and data analysis, leveraging Python to implement nine distinct analyses, multiple data filters, figure reproduction for publication, and automated HTML report generation. The tool was packaged as a pure Python, noarch module, adhering to bioconda distribution standards and supporting reproducible research workflows. Designed as a companion to the University of Michigan Single-Molecule-Sequencing lab’s end_reason paper, this work enhanced accessibility and scalability of ONT dataset analysis, facilitating cross-team collaboration and improving data quality assessment in research pipelines.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
1Total
Bugs
0
Commits
1
Features
1
Lines of code
84
Activity Months1
Your Network
862 peopleSame Organization
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Work History
May 2026
1 Commits • 1 Features
May 1, 2026May 2026: Delivered a major capability for Oxford Nanopore end_reason metadata analysis via a new CLI (ont-end-reason) integrated in bioconda/bioconda-recipes. Implemented 9 analyses (distribution, length, quality with Gaussian Mixture Model, temporal, hypothesis tests, Bayesian UMC posterior, signal trace, SMA metrics, tables), 4 filters, 4 paper figure reproducers, and HTML reports. The tool serves as a companion to the University of Michigan Single-Molecule-Sequencing lab end_reason paper. It is a pure Python, noarch package and was prepared for bioconda distribution; initial submission to conda-forge was superseded due to dependency constraints (pod5 and pysam are bioconda-only). This work aligns with bioconda packaging practices and enhances reproducibility and accessibility of end_reason analyses for ONT datasets.
1 Commits • 1 Features
May 1, 2026May 2026: Delivered a major capability for Oxford Nanopore end_reason metadata analysis via a new CLI (ont-end-reason) integrated in bioconda/bioconda-recipes. Implemented 9 analyses (distribution, length, quality with Gaussian Mixture Model, temporal, hypothesis tests, Bayesian UMC posterior, signal trace, SMA metrics, tables), 4 filters, 4 paper figure reproducers, and HTML reports. The tool serves as a companion to the University of Michigan Single-Molecule-Sequencing lab end_reason paper. It is a pure Python, noarch package and was prepared for bioconda distribution; initial submission to conda-forge was superseded due to dependency constraints (pod5 and pysam are bioconda-only). This work aligns with bioconda packaging practices and enhances reproducibility and accessibility of end_reason analyses for ONT datasets.
May 2026
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Quality Metrics
Correctness100.0%
Maintainability100.0%
Architecture100.0%
Performance100.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
Python
Technical Skills
BioinformaticsCLI DevelopmentData Analysis
Repositories Contributed To
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