populationgenomics/production-pipelines
Nov 2025 – Nov 2025
1 Month active
Languages Used
Python
Technical Skills
Python scriptingbioinformaticscloud computingcommand line toolsdata processingfile handling
Michael Harper
PROFILE
Michael Harper
Developed and delivered an end-to-end UBAM processing and kinetics removal pipeline for the populationgenomics/production-pipelines repository, enabling automated handling of PacBio ubam files sourced from Google Cloud Storage. Leveraging Python scripting and command line tools such as samtools, the solution removed kinetic data and outputted cleaned BAM files to a specified directory. The work included robust file handling, standardized output naming, and path corrections to streamline downstream data processing and reduce manual intervention. By focusing on reproducibility and clarity, the pipeline improved data quality and facilitated smoother integration with subsequent bioinformatics analytics, enhancing overall pipeline stability and usability.
Overall Statistics
Feature vs Bugs
100%Features
Repository Contributions
5Total
Bugs
0
Commits
5
Features
1
Lines of code
72
Activity Months1
Your Network
19 peopleSame Organization
@populationgenomics.org.au12
Shared Repositories
7
Work History
November 2025
5 Commits • 1 Features
Nov 1, 2025Month 2025-11 — Major feature delivered for populationgenomics/production-pipelines. Implemented the UBAM processing and kinetics removal pipeline enabling end-to-end handling of PacBio ubam files from Google Cloud Storage, removal of kinetic data via samtools, and saving cleaned BAMs to a defined output directory. Standardized output naming and path handling to improve downstream usability and clarity (changing extensions to .bam and naming conventions like '_no_kinetics_bam'). This work enhances data quality, reproducibility, and pipeline stability, reducing manual intervention and enabling smoother integration with downstream analytics.
5 Commits • 1 Features
Nov 1, 2025Month 2025-11 — Major feature delivered for populationgenomics/production-pipelines. Implemented the UBAM processing and kinetics removal pipeline enabling end-to-end handling of PacBio ubam files from Google Cloud Storage, removal of kinetic data via samtools, and saving cleaned BAMs to a defined output directory. Standardized output naming and path handling to improve downstream usability and clarity (changing extensions to .bam and naming conventions like '_no_kinetics_bam'). This work enhances data quality, reproducibility, and pipeline stability, reducing manual intervention and enabling smoother integration with downstream analytics.
November 2025
Activity
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Quality Metrics
Correctness100.0%
Maintainability96.0%
Architecture96.0%
Performance96.0%
AI Usage20.0%
Skills & Technologies
Programming Languages
Python
Technical Skills
Python scriptingbioinformaticscloud computingcommand line toolsdata processingfile handlingscripting
Repositories Contributed To
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