frogs_remove_chimera

frogs_remove_chimera removes PCR chimeras from amplicon and metagenomic sequencing data to improve the accuracy of downstream taxonomic profiling and phylogenetic inference.

Key Features:

• Chimera detection and removal: Identifies and eliminates chimeric sequences within each sample to preserve sequence integrity for downstream analysis.
• Galaxy integration: Executes chimera-detection and removal workflows using the Galaxy platform.
• Galaxy API / Bioblend communication: Interacts with Galaxy through its API or the Bioblend library for job submission and management.
• Integration with external services: Integrates workflow outputs with MetaGenSense and NGphylogeny.fr for downstream metagenomic and phylogenetic analyses.
• Resource management on Institut Pasteur cluster: Leverages Galaxy to manage computational resources on the Institut Pasteur cluster.

Scientific Applications:

• Metagenomics: Removal of PCR chimeras supports accurate taxonomic profiling and functional annotation in metagenomic and amplicon sequencing studies.
• Phylogenetic analysis: Ensures input sequences for phylogenetic inference are free of chimeric artifacts, improving evolutionary analyses.

Methodology:

Runs chimera-detection and removal workflows on Galaxy, communicates with Galaxy via its API or the Bioblend library, and manages execution on the Institut Pasteur cluster while exporting results for integration with MetaGenSense and NGphylogeny.fr.