Citations¶

If you use TaxTriage in your research, please cite the following:

TaxTriage¶

Merritt, Brian and Ratcliff, Jeremy D and Ta, Stanley and Osis, Gunars and Mauldin, Matthew R. and Thielen, Peter M.
TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection.
Bioinformatics 2026. doi: 10.1093/bioinformatics/btag119

BibTeX:

@article{Merritt2026taxtriage,
  title={TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection},
  author={Merritt, Brian and Ratcliff, Jeremy D and Ta, Stanley and Osis, Gunars and Mauldin, Matthew R and Thielen, Peter M},
  journal={Bioinformatics},
  year={2026},
  doi={10.1093/bioinformatics/btag119}
}

Zenodo:

Nextflow¶

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C.
Nextflow enables reproducible computational workflows.
Nat Biotechnol. 2017 Apr 11;35(4):316 - 319. doi: 10.1038/nbt.3820. PMID: 28398311.

Pipeline Tools¶

FastQC¶

Andrews, S. (2010). FastQC: a quality control tool for high throughput sequence data.
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

MultiQC¶

Ewels P, Magnusson M, Lundin S, Käller M.
MultiQC: summarize analysis results for multiple tools and samples in a single report.
Bioinformatics. 2016 Oct 1;32(19):3047 - 8. doi: 10.1093/bioinformatics/btw354. PMID: 27312411.

Software Packaging and Containerization¶

Anaconda¶

Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016.
https://anaconda.com

Bioconda¶

Grüning B, Dale R, Sjödin A, et al.
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nat Methods. 2018 Jul;15(7):475 - 476. doi: 10.1038/s41592-018-0046-7. PMID: 29967506.

BioContainers¶

da Veiga Leprevost F, Grüning B, Aflitos SA, et al.
BioContainers: an open-source and community-driven framework for software standardization.
Bioinformatics. 2017 Aug 15;33(16):2580 - 2582. doi: 10.1093/bioinformatics/btx192. PMID: 28379341.

Docker¶

Merkel, D. (2014). Docker: lightweight Linux containers for consistent development and deployment.
Linux Journal, 2014(239), 2.

Singularity¶

Kurtzer GM, Sochat V, Bauer MW.
Singularity: Scientific containers for mobility of compute.
PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. PMID: 28494014.

MicroBERT (Optional Module)¶

See preprint at 10.1101/2025.08.21.671544 for the MicroBERT genomic language model methodology.