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Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake.

Luke R Thompson1,2, Sean R Anderson1,2, Paul A Den Uyl3

  • 1Northern Gulf Institute, Mississippi State University, Mississippi State, MS 39762, USA.

Gigascience
|July 28, 2022
PubMed
Summary

Tourmaline automates environmental DNA (eDNA) metabarcoding analysis using QIIME 2, streamlining diversity surveys. This Python workflow enhances data reproducibility and accessibility for ecological research.

Keywords:
amplicon sequencingeDNAenvironmental DNAmeta-analysismetabarcodingmicrobiome

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Area of Science:

  • Environmental genomics
  • Bioinformatics
  • Ecology

Background:

  • Amplicon sequencing (metabarcoding) is crucial for surveying environmental community diversity.
  • QIIME 2 is a popular, functional software for amplicon data analysis.
  • Current QIIME 2 analyses lack automation, hindering efficiency and data sharing.

Purpose of the Study:

  • To develop an automated workflow for QIIME 2-based amplicon data analysis.
  • To improve efficiency, standardization, and reproducibility in metabarcoding studies.
  • To facilitate meta-analysis and sharing of environmental diversity data.

Main Methods:

  • Developed Tourmaline, a Python-based workflow using Snakemake and QIIME 2.
  • Implemented DADA2 or Deblur for denoising, followed by taxonomic assignment.
  • Included diversity analyses (alpha, beta) and automated HTML report generation.
  • Incorporated features like multi-core support, quality-based trimming, and sequence filtering.

Main Results:

  • Tourmaline successfully processed a 16S ribosomal RNA amplicon dataset.
  • Demonstrated utility for parameter optimization and interactive visualization.
  • Generated comprehensive HTML reports linking to QIIME 2 viewer and notebooks.

Conclusions:

  • Automated workflows like Tourmaline accelerate amplicon data analysis.
  • Tourmaline reduces the time from data generation to actionable ecological insights.
  • The workflow enhances reproducibility and accessibility of metabarcoding results.