converter_genbank_to_fasta
converter_genbank_to_fasta converts GenBank-format files into FASTA sequences for use in downstream bioinformatics analyses.
Key Features:
- Format Conversion: Transforms GenBank files into FASTA format for sequence-based analyses.
- Galaxy Integration: Operates within the Galaxy execution engine to run conversion tasks.
- API/Library Interface: Communicates with Galaxy via the Galaxy API or the Bioblend library to submit jobs.
- Execution Environment: Executes conversion jobs on the Institut Pasteur computational cluster.
Scientific Applications:
- Sequence Alignment: Provides FASTA sequences required for sequence alignment workflows.
- Phylogenetic Analysis: Prepares sequences for phylogenetic tree reconstruction.
- Metagenomic Studies: Enables inclusion of sequences in metagenomic analyses that require FASTA inputs.
Methodology:
Submits conversion jobs to Galaxy via the Galaxy API or Bioblend and executes them on the Institut Pasteur cluster.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Publications
Mareuil F, Doppelt-Azeroual O, Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services. Unknown Journal. 2017. doi:10.7490/f1000research.1114334.1.
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. 2016;44(W1):W3-W10. doi:10.1093/nar/gkw343. PMID:27137889. PMCID:PMC4987906.