listannotation
listannotation extracts counts of genes, rRNA, and tRNA from genomic annotation files to characterize annotation composition.
Key Features:
- Annotation File Analysis: Processes annotation files to extract the number of genes, rRNA, and tRNA present.
- Integration with Galaxy@Pasteur: Leverages Galaxy as an execution engine to run analyses on the Institut Pasteur cluster.
- Web Service Compatibility: Communicates with Galaxy using the Galaxy API or the Bioblend library.
Scientific Applications:
- Genomic Research: Provides annotation summaries that aid interpretation of sample genetic composition for genomics and molecular biology studies.
- Metagenomics: Supplies compositional information to support metagenomic workflows, including integration with MetaGenSense.
- Phylogenetic Studies: Contributes detailed annotation information for workflows that include phylogenetic tools such as NGphylogeny.fr.
Methodology:
Processes annotation files using Galaxy's execution capabilities and exchanges data with Galaxy via the Galaxy API or the Bioblend library, executing 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
Data retrieval
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.