Section outline

  • Before you can work with your data in PlutoF, you need to process your raw sequence files to generate Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs).

    Please Note: Processing raw sequence data happens outside of the PlutoF platform and is not covered directly in this tutorial.

    To help you get started with your bioinformatic workflow, here are three popular and reliable tools you can use:

    • PipeCraft2 - A user-friendly, cross-platform graphical interface (GUI) tool designed for metabarcoding data analyses. It offers ready-to-run pipelines as well as individual processing steps. Tip: Dedicated workflows developed through the Biodiversity Genomics Europe project can be explored at the Bioscanflow Documentation. These bioinformatic workflows have also been implemented in PipeCraft2.

    • QIIME 2 - A comprehensive, widely-used suite of plugins and bioinformatics methods. It is fantastic for performing deep microbiome analyses complete with interactive visualisations and robust statistical tools.

    • DADA2- A fast and powerful software package specifically designed to accurately model amplicon errors and infer exact ASVs straight from your raw sequencing data. Choose the tool that best fits your experience level and project requirements to generate your representative sequences, and you'll be ready to bring them into PlutoF!