sabund

sabund generates Sabund and Rabund files from CD-HIT cluster outputs to quantify sequence abundances for metagenomic and microbial community analyses.

Key Features:

• CD-HIT input: Processes CD-HIT cluster output files as the primary input for downstream analysis.
• Output formats: Produces Sabund and Rabund files representing cluster-level abundance data.
• Abundance estimation: Estimates the abundance of each cluster in the dataset from sequence counts.
• Galaxy integration: Integrates with the Galaxy platform for workflow execution.
• Galaxy API and Bioblend: Uses the Galaxy API and the Bioblend library for programmatic communication and workflow control.
• Compute execution: Executes workflows on the Institut Pasteur compute cluster.

Scientific Applications:

• Metagenomic profiling: Quantifies sequence abundances for characterization of metagenomic samples.
• Microbial ecology studies: Supports analysis of community composition and dynamics via cluster abundance data.
• Comparative genomics: Enables comparison of sequence diversity and abundance across samples or conditions.
• Pathogen detection: Facilitates identification and relative quantification of potential pathogens within complex communities.

Methodology:

Processes CD-HIT cluster outputs, performs cluster abundance calculation, generates Sabund and Rabund files, and uses the Galaxy API with Bioblend to execute workflows on the Institut Pasteur cluster.