genbank_convertor

genbank_convertor converts GenBank and EMBL sequence files into .ffn, .faa, ptt, and Sequin-compatible formats for downstream genomic and phylogenetic analyses.

Key Features:

• Format Conversion: Converts GenBank and EMBL sequence files into .ffn (gene), .faa (protein FASTA), ptt (protein table), and Sequin-compatible files.
• Platform Integration: Integrates with the Galaxy platform as an execution environment for running conversion workflows.
• API-Based Execution: Executes conversion jobs via Galaxy API calls or the Bioblend library to manage tasks on the Institut Pasteur compute cluster.

Scientific Applications:

• Genomic research: Prepares sequence and annotation files for genome-scale analyses.
• Metagenomic data analysis: Produces .ffn, .faa, and ptt outputs used in metagenomic workflows.
• Phylogenetic studies: Generates protein and gene FASTA files for phylogenetic and evolutionary analyses.
• Sequence-based investigations: Provides standardized file formats for downstream sequence analyses and integration with other bioinformatics tools.

Methodology:

Converts GenBank and EMBL inputs into .ffn, .faa, ptt, and Sequin-compatible files and runs these conversions within the Galaxy framework using Galaxy API calls or the Bioblend library to submit and manage jobs on the Institut Pasteur compute cluster.