Welcome to Petri: 16S metagenomics analysis pipeline’s documentation!

Flomics’ Petri: 16S metagenomics NGS Data analysis pipeline was developed to produce interpretable results from 16S amplicon sequencing NGS-based experiments, without the need to learn bioinformatics.

The user will obtain from raw, unprocessed sequencing files curated outputs such as OTUs and ASVs characterization of the sample. The pipeline accepts Illumina data (single-end or paired-end reads) obtained using various kits, with new kits being added as they become available. Support for PacBio and IonTorrent sequencing data is experimental at this point.

Check out the Usage section for further information.

Note

This project is under active development.

Contents

• Usage
  • Input
  • Options
    • Sequencing kit
    • Sequencing type
    • Skip trimming
    • Taxonomy database
    • Sequencing files
  • Accepted sample names
  • Grouping
  • Launching
• Glossary
• Pipeline overview
• Output
  • FastQC
  • Cutadapt
  • DADA2
  • QIIME2
  • Krona plots
  • Sample report
  • Analysis report
  • MultiQC
  • Pipeline information
• FAQ
  • Why …
    • …does the scale of the heatmap go from -2 to 2?
    • …do the names of the features in the heatmap have several semicolons on them (“;;;”)?
  • How …
    • …to interpret alpha-diversity metrics?
    • …to interpret beta-diversity metrics?
• References
  • Credits & Acknowledgements
  • Tools & Assets