microbiome-amplicon

What problem does it solve?

Amplicon microbiome analysis often requires chaining multiple steps (denoising, taxonomic assignment, diversity analyses) across disparate tools, which can be error-prone and time-consuming. This skill provides a cohesive, repeatable workflow to move from raw reads to interpretable abundance tables and diversity summaries with clear guidance and provenance.

Core Features & Use Cases

• Denoising and Amplicon Inference: generate ASV/OTU-level counts from raw marker-gene data.
• Taxonomy Assignment: assign taxonomic labels using suitable reference databases.
• Diversity Analysis: compute alpha and beta diversity metrics and visualize group differences.
• Differential Abundance: support group-level comparisons with appropriate statistical approaches.
• Use Case: analyze 16S rRNA gene data to compare microbial communities across treatment groups.

Quick Start

Use the starter pattern to process a raw amplicon dataset and generate ASV tables and diversity plots.