Starting from 16S amplicon sequencing data and a sample metadata table: quality control, feature table construction, diversity analysis, differential analysis and visualisation.
Organise FASTQ files, sample group information and the experimental design table.
Sample IDs in the metadata must match the sequencing files exactly.
Perform sequence QC, denoising, chimera removal and feature sequence generation.
Choose truncation lengths based on the quality plots.
Generate an ASV/OTU feature table and assign taxonomy.
State the taxonomy database and version in the methods section.
Compute alpha diversity, beta diversity and differences in community structure.
Statistical tests must match the grouping design.
Run differential abundance analysis and draw composition plots, heatmaps, PCoA plots and box plots.
Interpret differential results in light of their biological meaning.
