Pyrene-adapted Rhodococcus ruber strain

Bioinformatics scripts developed during the adaptive laboratory evolution of Rhodococcus ruber under high pyrene concentrations

Features

• Genome assembly statistics
• GC content calculations
• VCF variant parsing
• Mutation mapping
• Comparative genome analysis

Example Workflow

Hybrid genome assembly
        ↓
Annotation
        ↓
Genome comparison
        ↓
Variant detection
        ↓
Biological interpretation

Requirements

• Python 3.10+
• Biopython
• R

Author

Gabriela Calcáneo-Hernández

Postdoctoral researcher

UNAM

Original experimental data are available in Mendeley Data at 10.17632/864zyxk8r7.1

Skills Demonstrated

• Comparative genomics
• Genome assembly analysis
• Variant calling and VCF processing
• Mutation mapping
• Python scripting
• R statistical analysis
• Data visualization
• Bioinformatics workflow development

Citation

If you use these scripts, please cite:

Calcáneo-Hernández et al., (2026) Adaptive laboratory evolution of the hydrocarbonoclastic marine strain Rhodococcus ruber MSA14 to high pyrene concentrations

Development Notes

Some scripts were developed with the assistance of AI coding tools and subsequently reviewed, tested, and adapted by the author.