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crabs-A software program to generate curated reference databases for metabarcoding sequencing data.

Gert-Jan Jeunen1, Eddy Dowle1, Jonika Edgecombe1

  • 1Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.

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Summary
This summary is machine-generated.

A new software called crabs (Creating Reference databases for Amplicon-Based Sequencing) helps researchers build custom eukaryotic reference databases. This improves the accuracy of biodiversity assessments using metabarcoding sequencing data.

Keywords:
aDNAancient DNAeDNAenvironmental DNApythonreference database curationtaxonomy assignment

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Area of Science:

  • Biodiversity research
  • Bioinformatics
  • Genomics

Background:

  • Metabarcoding studies generate vast amounts of biodiversity data.
  • Accurate taxonomic assignment relies heavily on high-quality reference databases.
  • Existing tools for creating custom eukaryotic reference databases are limited.

Purpose of the Study:

  • To introduce crabs, a software package for creating custom, curated eukaryotic reference databases.
  • To enhance the reliability and accuracy of taxonomic assignment in metabarcoding research.

Main Methods:

  • Utilizes multiple online repositories (NCBI, BOLD, EMBL, MitoFish) for sequence retrieval.
  • Performs in silico PCR and global alignments to identify target amplicon regions.
  • Applies multiple filtering parameters for database curation (dereplication, length, quality, taxonomy).
  • Includes visualization tools for database assessment (diversity, completeness, resolution).

Main Results:

  • crabs provides a versatile solution for generating user-specified genetic marker databases.
  • The software facilitates immediate use of created databases in taxonomy assignment pipelines.
  • Database creation is streamlined through automated downloading, curation, and export functionalities.

Conclusions:

  • crabs empowers researchers to build custom reference databases, crucial for accurate biodiversity assessments.
  • The software addresses the scarcity of tools for eukaryotic reference database generation.
  • crabs is readily available via Docker, conda, and GitHub for widespread adoption.