detaxizer

What problem does it solve?

nf-core/detaxizer helps researchers identify a target taxon in sequencing reads and optionally remove those reads without manual flag hunting or guesswork.

Core Features & Use Cases

• Taxon detection and removal: Classify reads with Kraken2 and/or bbduk, then filter or retain matches based on the selected taxon or taxonomic group.
• Optional preprocessing and validation: Clean reads with fastp before classification and confirm results with blastn when validation is required.
• Reproducible bioinformatics runs: Use samplesheets, pinned releases, and generated reference documentation to keep execution consistent across environments.
• Use case: A metagenomics analyst can process host-depletion datasets, generate downstream samplesheets, and produce traceable results for the next analysis step.

Quick Start

Use this Skill to run detaxizer on your samplesheet with the correct output directory and any optional classification, filtering, or validation settings you need.