clc_cas_to_sam

clc_cas_to_sam converts CAS (CLC Sequence Viewer) files into SAM or BAM formats to enable interoperability of CLC-derived alignment data with SAM/BAM-based genomic analysis workflows.

Key Features:

• File Conversion: Transforms CAS files from CLC Sequence Viewer into SAM or BAM formats for standard alignment data representation.
• Galaxy@Pasteur integration: Executes conversions within the Galaxy@Pasteur framework leveraging its computational infrastructure.
• Galaxy API / Bioblend execution: Uses the Galaxy API or the Bioblend library to communicate with the Galaxy instance at Institut Pasteur and submit jobs to cluster and storage resources.

Scientific Applications:

• Metagenomics: Enables integration of CLC-derived metagenomic alignment data with SAM/BAM-based metagenomic analysis tools.
• Genomic Research: Supports downstream analyses such as variant calling, sequence assembly, and comparative genomics by providing standard SAM/BAM alignment files.

Methodology:

Operates within the Galaxy@Pasteur framework to perform CAS-to-SAM/BAM conversions and uses the Galaxy API or the Bioblend library to submit and execute conversion jobs on Institut Pasteur computational resources.