fqextract
fqextract extracts subsets of FASTQ reads to enable targeted selection of sequencing reads for downstream genomic, metagenomic, and phylogenetic analyses within the Galaxy platform.
Key Features:
- FASTQ subsetting: Extracts subsets of FASTQ reads for focused downstream analysis.
- Galaxy integration: Integrates with the Galaxy execution engine and is deployed within the Galaxy@Pasteur instance to manage and process large-scale bioinformatics workflows.
- API and library interfacing: Interfaces with Galaxy's API or the Bioblend library to initiate and control data extraction tasks.
- Cluster execution: Executes data extraction tasks on the Institut Pasteur cluster.
Scientific Applications:
- Metagenomic Data Analysis: Used in workflows such as MetaGenSense to extract FASTQ subsets for analysis of microbial communities or specific genomic regions.
- Phylogenetic Studies: Supports dataset preparation for phylogenetic analysis workflows such as NGphylogeny.fr by selecting relevant sequences from FASTQ data.
Methodology:
Interfaces with Galaxy's API or the Bioblend library to execute FASTQ read extraction tasks on the Institut Pasteur cluster.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Added:
- 12/19/2016
- Last Updated:
- 8/27/2025
Operations
Data 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.