fastaextract
fastaextract extracts or excludes specific sequences from multifasta files using a dataset of identifiers to enable targeted sequence selection for genomic and metagenomic analyses.
Key Features:
- Sequence Extraction/Exclusion: Selectively extracts or excludes one or more sequences from multifasta files based on provided identifiers.
- Identifier Dataset Handling: Uses a dataset of identifiers to specify sequences to include or exclude.
- Galaxy Integration: Operates within the Galaxy execution environment to run alongside other Galaxy tools.
Scientific Applications:
- Metagenomic Data Analysis: Enables extraction of genes or regions of interest from complex metagenomic multifasta datasets.
- Phylogenetic Studies: Aids preparation of sequence sets for phylogenetic analysis by excluding irrelevant sequences.
Methodology:
Communicates with Galaxy via the Galaxy API using the Bioblend library to submit and manage 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
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.
1.Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Äech M, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research [Internet]. 2016 May 2;44(W1):W3â10. Available from: http://dx.doi.org/10.1093/nar/gkw343