Pipeline overview
The pipeline is built using Nextflow and processes data in the following steps:
FastQC : Read quality control.
Cutadapt : Primer trimming.
DADA2 : Infer Amplicon Sequence Variants (ASVs) and taxonomic classification.
QIIME2 : Secondary analysis on diversity results.
Taxonomic classification: Taxonomical classification of ASVs.
Relative abundance tables: Exported relative abundance tables.
Alpha diversity rarefaction curves: Rarefaction curves for quality control.
Diversity analysis: High level overview with different diversity indices.
Alpha diversity indices: Diversity within samples
Beta diversity indices: Diversity between samples (e.g. PCoA plots)
With all the intermediate outputs from the steps above, the pipeline produces several reports aggregating the results in a comprehensible and elegant manner:
Krona plots : Interactive visualization of the diversity within samples.
Sample reports: Aggregated report of all the relevant information for each sample (QC, ASVs present, etc).
Analysis report: Aggregated report of all the samples, containing alpha and beta-diversity measures and a clustered heatmap.
MultiQC :Interactive aggregated report of all the quality control metrics.
Finally, the pipelines takes all the aforementioned outputs and produces a easily downloadable ZIP file.