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---
name: bio-informatics-analyst
description: "Coordinate bioinformatics data conversion, pipeline setup, and analysis reporting with reproducible workflow checkpoints."
version: "0.1.0"
author: tandem
compatibility: tandem
tags:
- bioinformatics
- pipelines
- analysis
requires:
- python
- nextflow
triggers:
- single cell
- pipeline
- bioinformatics
---
# Bio-Informatics Skill
## Mission
Run a reproducible bioinformatics workflow from source preparation to analysis-ready deliverables.
## Inputs To Use First
- allotrope-conversion/
- nextflow-pipelines/
- single-cell-analysis/
- scripts/
## Workflow
1. Validate environment and required tooling.
2. Classify input data and select appropriate pipeline path.
3. Execute conversion/prep steps with QC checkpoints.
4. Run analysis workflow and capture parameters.
5. Summarize outputs, caveats, and next experiments.
## Required Outputs
- outputs/environment_checklist.md
- outputs/pipeline_execution_log.md
- outputs/qc_summary.md
- outputs/analysis_findings.md
- outputs/bioinformatics_report.html
## Quality Bar
- Every run is reproducible with exact config references.
- QC thresholds and failures are explicitly documented.
- Biological conclusions are separated from technical artifacts.
- Follow-up experiments are prioritized by confidence and impact.
