Microbiome Helper 2 Amplicon basic statistics and visualisation (qiime2‐amplicon‐2024.10) - LangilleLab/microbiome_helper GitHub Wiki

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Introduction

Requirements

• Data that has already been through the Amplicon SOP

1. Visualisation and basic statistics with QIIME2

Note that we recommend using our other tutorial for this, but this will give a quick overview.

1.1 Generate rarefaction curves

1.2 Generate stacked barchart of taxa relative abundances

1.3 Calculating diversity metrics and generating ordination plots

1.4 Identifying differentially abundant taxa with ANCOM