frogs_biom_to_stdbiom
frogs_biom_to_stdbiom converts FROGS BIOM files into a standard BIOM format to enable interoperability of metagenomic and phylogenetic analysis workflows.
Key Features:
- Format Conversion: Converts data from the FROGS BIOM format to the standard BIOM format for compatibility with BIOM-based tools and databases.
- Galaxy integration: Executes within the Galaxy platform and is deployable on Galaxy instances such as Galaxy@Pasteur.
- Scalability: Is part of a Galaxy@Pasteur tool suite of over 280 tools processing approximately 3000 registered-user jobs and 1500 anonymous-user jobs per month, supporting large-scale data processing.
Scientific Applications:
- Metagenomic Data Analysis: Provides standardized BIOM inputs for metagenomic workflows and projects such as MetaGenSense.
- Phylogenetic Studies: Supplies compliant BIOM-format input for phylogenetic analyses and services such as NGphylogeny.fr.
Methodology:
Communication with Galaxy is managed via the Galaxy API or the Bioblend library, centralizing resource management and enabling access to storage and computational resources on the Institut Pasteur cluster.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Formatting
Inputs
Outputs
Publications
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.
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.