readfastafile
readfastafile sorts FASTA-formatted sequence files composed of alphanumerical characters representing nucleotide or protein sequences to organize data for downstream bioinformatics analyses.
Key Features:
- FASTA file sorting: Organizes FASTA-formatted nucleotide and protein sequences by sorting sequence records.
- Galaxy integration: Integrates with the Galaxy@Pasteur instance and uses Galaxy as the execution engine for computational tasks.
- API communication: Interacts with Galaxy via the Galaxy API or the Bioblend library to execute jobs on the Institut Pasteur cluster.
Scientific Applications:
- Metagenomic data analysis: Provides sorted FASTA inputs for metagenomics workflows such as the MetaGenSense LIMS.
- Phylogenetic studies: Supplies organized FASTA files for downstream phylogenetic workflows, including services like NGphylogeny.fr.
Methodology:
Performs FASTA sorting within the Galaxy environment, using Galaxy as the execution engine and communicating via the Galaxy API or Bioblend to run jobs 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
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.