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  1. Home
  3. Pr2-wormifier: A Bioinformatics Pipeline To Create Custom Reference Databases For Improved Metabarcoding Of Marine Protists.
  1. Home
  3. Pr2-wormifier: A Bioinformatics Pipeline To Create Custom Reference Databases For Improved Metabarcoding Of Marine Protists.

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pr2-Wormifier: A Bioinformatics Pipeline to Create Custom Reference Databases for Improved Metabarcoding of Marine

Stefanie Knell1,2, Juliane Romahn1,2,3, Miklós Bálint1,2,3

  • 1Justus Liebig University Giessen, Giessen, Germany.

Molecular Ecology Resources
|June 23, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

pr2-wormifier creates custom marine protist databases for environmental DNA (eDNA) studies. This improves taxonomic identification accuracy in metabarcoding, addressing limitations of existing resources.

Keywords:
18S rRNAWoRMsciliateenvironmental DNAsedaDNAtaxonomic affiliation

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Area of Science:

  • Marine biology
  • Bioinformatics
  • Genomics

Background:

  • Metabarcoding of environmental DNA (eDNA) and sedimentary ancient DNA (sedaDNA) is crucial for marine community assessment.
  • Existing reference databases for 18S rRNA gene metabarcoding, especially for protists, lack comprehensiveness and taxonomic resolution.
  • This limits the accuracy of biodiversity monitoring and paleoenvironmental reconstructions.

Purpose of the Study:

  • To introduce pr2-wormifier, a bioinformatics pipeline for generating customized and improved 18S rRNA-based reference databases.
  • To enhance taxonomic assignments for marine protists, including ciliates and dinoflagellates, at genus and species levels.
  • To address limitations of current databases, such as low resolution and missing taxa.

Main Methods:

  • The pr2-wormifier pipeline integrates sequences from PR2 and NCBI databases.
  • It incorporates taxonomic information from the World Register of Marine Species (WoRMS) and AlgaeBase.
  • The pipeline was benchmarked using a Baltic Sea sedimentary ancient DNA dataset.

    • Main Results:

    • pr2-wormifier successfully generated customized reference databases for marine protists.
    • The customized database improved taxonomic assignments at genus and species levels compared to using PR2 alone.
    • The pipeline maintained taxonomic consistency and quality in sequence identification.

    Conclusions:

    • pr2-wormifier provides a flexible and scalable solution for creating tailored reference databases.
    • It enhances the accuracy and resolution of protist identification in metabarcoding studies.
    • This tool facilitates more reliable biodiversity assessments in marine and paleoenvironmental research.