kronaextract
kronaextract extracts taxonomic read lists and BLAST offsets from Krona XML files (e.g., generated by rankoptimizer) to support targeted analysis of high-throughput next-generation DNA sequencing datasets.
Key Features:
- Data extraction: Extracts lists of reads and their corresponding BLAST offsets for specified taxonomic names from Krona XML files.
- Galaxy integration: Provides integration with the Galaxy Project.
- Large-scale data handling: Handles extraction from large Krona XML files produced by next-generation DNA sequencing workflows.
Scientific Applications:
- Microbial community analysis: Identifies reads associated with specific taxa within complex samples using Krona XML outputs.
- Metagenomic studies: Improves targeted taxon-level analysis by extracting reads and BLAST offsets for downstream validation or reanalysis.
- Ecological and evolutionary research: Provides taxon-level read and offset data to support studies of species distribution and abundance.
Methodology:
Parses Krona XML files and extracts read lists and BLAST offsets based on user-specified taxonomic names or criteria.
Topics
Collections
Details
- Maturity:
- Mature
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 12/19/2016
- Last Updated:
- 11/25/2024
Operations
Data Inputs & Outputs
Read mapping
Outputs
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.
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.