Pipeline overview

Flowchart of the pipeline's processing steps

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.