bam2roi

bam2roi extracts regions of interest (ROIs) from BAM files to enable focused downstream genomic analyses such as variant calling, expression analysis, and targeted sequencing.

Key Features:

• Integration with Galaxy Platform: Operates within the Galaxy framework to execute ROI-generation workflows from BAM inputs.
• Galaxy API / Bioblend integration: Communicates with Galaxy using the Galaxy API or the Bioblend library for workflow control and data exchange.
• Execution on Galaxy@Pasteur cluster: Runs workflows on the Institut Pasteur high-performance computing resources via the Galaxy@Pasteur instance.
• Centralized server access: Centralizes access to computational resources and storage through a single server interface for workflow execution and management.

Scientific Applications:

• Variant calling and expression analysis: Produces ROIs from BAM files to support variant calling, expression analysis, and targeted sequencing workflows.
• Genomics, metagenomics and phylogenetics: Enables selection of specific genomic regions relevant to genomics, metagenomics, and phylogenetics studies.

Methodology:

Communicates with the Galaxy platform via its API or the Bioblend library and launches workflows on the Galaxy@Pasteur cluster, centralizing access and management through a single server.