PATHDET

Version 2.0

  PATHDET is a web application for “PATHogen DETection” from extracellular DNA/RNA viahigh-throughput sequencing data given by users. The PATHDET pipeline, step-by-step procedures described in the figure below, detects pathogenic microorganisms from the organisms (humans, animals, plants, etc.) with infections. Also, the pipeline is applicable to investigation of contaminants of microorganisms from the samples of biological experiments and clinical instruments. Users can obtain a list of the microorganisms populating in the sample through the PATHDET execution, which initiates by uploading the sequence data to a web server. The PATHDET provides two types of reports: an interactive result view on a web browser and a downloadable detailed report. Additionally, users can access a brief summary of the rapid pathogen search, which is usually available in ten minutes.

PATHDET summary

Release Notes

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Citation

Please cite the following URL if you are using PATHDET:

https://pathdet.hgc.jp


Disclaimer


Publications

Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study.
Torii Y, Horiba K, Hayano S, et al.
BMC Pediatr. 2020 Oct 15;20(1):482. doi: 10.1186/s12887-020-02380-7. GO

Temporal dynamics of the plasma microbiome in recipients at early post-liver transplantation: a retrospective study.
Okumura T, Horiba K, Kamei H, et al.
BMC Microbiol. 2021 Apr 6;21(1):104. doi: 10.1186/s12866-021-02154-w. GO

Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases.
Horiba K, Torii Y, Okumura T, et al.
Open Forum Infect Dis. 2021 (in press).

Pediatric sepsis cases diagnosed with group B streptococcal meningitis using next-generation sequencing: a report of two cases
Horiba K, Suzuki M, Tetsuka N, et al.
BMC Infect Dis. 2021 Jun 5;21(1):531. doi: 10.1186/s12879-021-06231-3. GO



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Contact

Send e-mail to pathdet.message@gmail.com


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This website is provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo