Run nf-core/detaxizer to identify and remove target taxa from genomic FASTQ data.
npx skills add https://github.com/danilomonge/nf-claw --skill detaxizer
Please help me install this Agent Skill. Skill: detaxizer Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/detaxizer Command: npx skills add https://github.com/danilomonge/nf-claw --skill detaxizer
nf-core/detaxizer helps researchers identify a target taxon in sequencing reads and optionally remove those reads without manual flag hunting or guesswork.
Use this Skill to run detaxizer on your samplesheet with the correct output directory and any optional classification, filtering, or validation settings you need.
High-intent search queries and answers about installing and using this skill.
Detaxizer removes target taxa from FASTQ data by running the nf-core/detaxizer pipeline, which classifies reads with Kraken2 and bbduk before filtering. It requires validated CSV samplesheets and pinned Nextflow releases to ensure reproducible host-depletion workflows.
The nf-core detaxizer pipeline is used for taxon detection and removal in metagenomics. It identifies target taxa in sequencing reads, optionally validates matches with blastn, and generates downstream samplesheets to prepare filtered data for subsequent analysis steps.
Yes, you can validate Kraken2 classification results with blastn within the detaxizer Nextflow pipeline. This optional validation step confirms taxonomic matches before read filtering, ensuring higher confidence in the target taxa identified in your FASTQ samples.
To process genomic FASTQ data with detaxizer, you must provide a validated CSV samplesheet as input. The Skill handles samplesheet-based preprocessing to ensure input metadata meets parameter constraints before running the Nextflow pipeline for taxon identification and removal.
Yes, the detaxizer pipeline supports fastp preprocessing to clean reads before taxonomic classification. This optional step improves classification accuracy by removing low-quality sequences before Kraken2 or bbduk analyze the FASTQ data for target taxa.
Running nf-core detaxizer requires validated CSV samplesheets, genomic FASTQ files, and a Nextflow execution environment. The pipeline enforces parameter constraints and uses pinned releases to maintain reproducible provenance for identifying and removing target taxa.
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