TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

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.