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Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.

Marius Welzel1, Anja Lange2, Dominik Heider1

  • 1Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany.

BMC Bioinformatics
|November 17, 2020
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Summary

Natrix is a new, open-source bioinformatics workflow that simplifies processing amplicon sequencing data. This user-friendly tool ensures reproducible analysis of microbial community diversity using Snakemake and Conda.

Keywords:
Amplicon Sequence VariantsAmplicon sequencingIlluminaOperational Taxonomic UnitsPiplineSnakemake

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Computational Biology

Background:

  • Amplicon sequencing reveals microbial diversity and ecological processes.
  • High-throughput sequencing generates large datasets requiring efficient bioinformatics pipelines.
  • Existing workflows often lack user-friendliness, scalability, and reproducibility.

Purpose of the Study:

  • To present Natrix, an open-source bioinformatics workflow for preprocessing amplicon sequencing data.
  • To provide a user-friendly, scalable, and reproducible solution for analyzing complex microbial communities.
  • To facilitate the sharing and adaptation of bioinformatics analysis rules.

Main Methods:

  • Developed Natrix, an open-source workflow using Snakemake for workflow management.
  • Integrated Conda for version control of software dependencies.
  • Included comprehensive analysis steps from quality assessment to taxonomic assignment.

Main Results:

  • Natrix preprocesses raw amplicon sequencing data, including quality assessment, read assembly, dereplication, chimera detection, and taxonomic assignment.
  • The workflow ensures reproducibility through Snakemake and version control via Conda.
  • Natrix is available on GitHub and as a Docker container.

Conclusions:

  • Natrix offers a user-friendly and highly extensible solution for processing Illumina amplicon data.
  • The workflow enhances the analysis of microbial community diversity.
  • Natrix promotes reproducible and scalable bioinformatics analyses.