bam_to_sam

bam_to_sam converts Binary Alignment/Map (BAM) files to Sequence Alignment/Map (SAM) format to provide a human-readable text representation of sequence alignments for downstream analyses such as variant calling and alignment inspection.

Key Features:

• Format Conversion: Transforms BAM files into SAM files, producing a text-based representation of sequence alignment data.
• Integration with Galaxy Platform: Operates within the Galaxy platform to enable execution as part of Galaxy workflows.
• Execution via Galaxy API: Invokes the conversion through the Galaxy API to enable programmatic execution and integration with other Galaxy tools on the Institut Pasteur instance.
• Resource Accessibility: Leverages the Institut Pasteur Galaxy cluster computational resources for storage and processing of large genomic datasets.

Scientific Applications:

• Genomic Data Analysis: Supports downstream tasks including variant calling, sequence alignment verification, and detailed inspection of sequencing results.
• Reproducible Research: Enables reproducible computational workflows by running within Galaxy workflow frameworks and via the Galaxy API.

Methodology:

The conversion is executed on the Galaxy platform using the Galaxy API and the platform's execution infrastructure, leveraging cluster resources to process large datasets while preserving data integrity.