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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

Brian Merritt1, Jeremy D Ratcliff1, Stanley Ta1

  • 1Johns Hopkins Applied Physics Laboratory, Laurel, MD 20723, United States.

Bioinformatics (Oxford, England)
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Summary

TaxTriage is a versatile pathogen identification workflow for DNA/RNA sequencing. It accurately identifies pathogens using multiple methods and offers flexible installation, enhancing diagnostic capabilities.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Pathogen Discovery

Background:

  • TaxTriage is a comprehensive workflow for pathogen identification from untargeted DNA/RNA sequencing data.
  • It integrates read classification, mapping, and de novo assembly for robust pathogen detection.
  • Flexible installation via Nextflow™ supports cloud and local deployments, including offline use.

Purpose of the Study:

  • To present TaxTriage, a novel bioinformatics workflow for pathogen identification.
  • To detail its methods, performance, and customization options for diverse diagnostic needs.
  • To provide a reproducible and accessible tool for public health and veterinary communities.

Main Methods:

  • Utilizes read classification, mapping, and de novo assembly approaches.
  • Compares sequencing data against curated pathogen databases and healthy cohort abundance data.
  • Employs Nextflow™ for flexible deployment (cloud/local) and generates Organism Discovery Reports.

Main Results:

  • Achieved performance comparable to cloud-based pipelines in detecting pathogens and co-infections.
  • Demonstrated similar sensitivity and increased specificity compared to alternatives.
  • Incorporated customization for improved performance across different host species.

Conclusions:

  • TaxTriage offers a powerful, flexible, and accurate solution for pathogen identification.
  • Its performance and customization features benefit both public health and veterinary diagnostics.
  • The workflow is freely available, promoting reproducible research and widespread adoption.