Run the nf-core/coproid pipeline for host DNA identification in paleofaeces samples.
npx skills add https://github.com/danilomonge/nf-claw --skill coproid
Please help me install this Agent Skill. Skill: coproid Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/coproid Command: npx skills add https://github.com/danilomonge/nf-claw --skill coproid
Coproid automates the analysis of complex Illumina metagenomic samples to help identify the true host signal in paleofaeces and related microbiome-rich material, avoiding manual flag hunting and release-specific confusion.
Ask me to run the coproid pipeline on your samplesheet with the required genome, kraken2, and sourcepredict inputs, and I will launch the pinned release into your chosen output directory.
High-intent search queries and answers about installing and using this skill.
Host DNA identification from paleofaeces metagenomic samples uses the nf-core/coproid pipeline to compare microbiome composition, endogenous host DNA, and source-prediction signals across Illumina reads. This automated approach applies source-prediction to pinpoint the true host without manual flag hunting.
Running a coproid host-identification workflow requires an Illumina samplesheet in CSV format, reference genome inputs, and kraken2 and sourcepredict reference tables. You must also specify an output directory and schema-validated parameters with an explicit Nextflow version control.
The nf-core coproid pipeline supports reproducible metagenomics analysis by running a pinned pipeline release bundled with the skill. This ensures standardized outputs, MultiQC summaries, and run metadata remain consistent across different analyses for traceable downstream reporting.
To process a faecal metagenomics study for host-identification results, provide sequencing reads and the required reference tables to the pipeline. The schema-validated inputs enforce correct parameter usage, allowing you to obtain results without inspecting upstream documentation.
You should use coproid for metagenomic host identification when working with complex Illumina faecal metagenomic samples, especially paleofaeces and microbiome-rich material. It is designed to resolve true host signals when manual flag hunting and release-specific confusion become problematic.
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