TaxTriage Documentation¶

See it first¶

Interactive report demo Example ODR (PDF) Pathogen sheet

The demo is a live report built from the example dataset, its the same artifact the pipeline writes at the end of a run, complete with live filters and sample QC flags you can edit in the browser. The ODR is the static PDF deliverable. The pathogen sheet is every organism TaxTriage can flag, searchable and filterable.

About TaxTriage¶

TaxTriage is a flexible, containerized bioinformatics pipeline designed to identify pathogens within complex samples (e.g., respiratory swabs, lesion swabs, whole blood) using untargeted DNA or RNA sequencing data. It supports short-read (Illumina) and long-read (ONT, PacBio) platforms, incorporating quality control, organism classification, read mapping, and a unified confidence metric for all identified organisms.

The final analysis output is an Organism Discovery Report (ODR) - 2 files (a PDF and an interactive HTML) with summaries of all intermediate data supporting pathogen identification. TaxTriage is designed for broad deployment and early-stage outbreak investigations and is not intended as a standalone diagnostic capability.

Section	Description
Installation	Install Nextflow, Docker, and Singularity
Quick Start	Run your first test pipeline in minutes
Samplesheet	Format and prepare your input samplesheet
Running the Pipeline	Commands, profiles, and execution modes
CLI Parameters	Full reference for all pipeline parameters
Pipeline Modules	Step-by-step breakdown of the workflow
Output	Understanding output files and directories
TASS Scoring	How the confidence score is calculated
Microbial Categories	Primary, Opportunistic, Potential, Commensal - what they mean and how to read them
In-Silico Simulation	Simulated read validation
Cloud & Seqera	Running on AWS with Nextflow Tower / Seqera
Geneious Plugin	Geneious Prime integration
Troubleshooting	FAQ and common errors
Contributing	How to contribute to TaxTriage
Citations	Tools and publications to cite

Pipeline Overview¶

TaxTriage ingests raw FASTQ data and processes it through the following major stages:

Read QC - FastQC / NanoPlot / pycoQC
Trimming - Trimgalore (Illumina) / Porechop (ONT); optional fastp / fastplong quality filtering with --enable_fastp (off by default)
Host Removal - Minimap2 against host reference
Metagenomics Classification - Kraken2 (+ Krona plots)
Top Hits Assignment - Selects organisms for alignment
Reference Preparation - Downloads assemblies from NCBI
Alignment - BWA-MEM2 (Illumina) / Minimap2 (ONT/PacBio)
Stats - Coverage, depth, MAPQ via samtools
TASS Scoring - Confidence metric calculation
Report Generation - MultiQC + Organism Discovery Report PDF

Collaborative Efforts¶

UW Madison - Geneious Prime Plugin¶

Dave O'Connor's Laboratory at the University of Wisconsin-Madison developed a custom Geneious Prime plugin to run TaxTriage analyses directly from within Geneious. See the Geneious Plugin page for details.

Citation¶

If you use TaxTriage, please cite:

Brian B. Merritt & Jeremy D. Ratcliff et. al, TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection. doi: 10.1093/bioinformatics/btag119/8571885

See the Citations page for the full list of tools to cite.