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.
Please cite the following if you are using PATHDET for short-read:
Horiba K, Torii Y, Okumura T, Takeuchi S, Suzuki T, Kawada JI, Muramatsu H, Takahashi Y, Ogi T, Ito Y. Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases. Open Forum Infect Dis. 2021 May 4;8(11):ofab223. doi: 10.1093/ofid/ofab223.
Please cite the following if you are using PATHDET for long-read:
Horiba K, Torii Y, Aizawa Y, Yamaguchi M, Haruta K, Okumura T, Suzuki T, Kawano Y, Kawada JI, Hara S, Saitoh A, Giske CG, Ogi T, Ito Y. Performance of Nanopore and Illumina metagenomic sequencing for pathogen detection and transcriptome analysis in infantile central nervous system infections. Open Forum Infect Dis. 2022 ofab504. doi: 10.1093/ofid/ofac504 .
- The users are responsible for all risks associated with the use of and the data transfer to PATHDET. PATHDET makes no legal liability for any claims or damages arising from the use of PATHDET.
- PATHDET is not responsible for the accuracy, equivalence, and completeness of the analysis results.
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.
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.
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 May 4;8(11):ofab223. doi: 10.1093/ofid/ofab223.
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.
Performance of Nanopore and Illumina metagenomic sequencing for pathogen detection and transcriptome analysis in infantile central nervous system infections
Horiba K, Torii Y, Aizawa Y, et al.
Open Forum Infect Dis. 2022 ofac504. doi: 10.1093/ofid/ofac504.
- Prior to uploading personal sequencing data to PATHDET, the users must remove the sequence reads derived from the individuals to a level unable to identify the personal information.
- The use of personal sequence data for PATHDET should be approved by the institutional review board and by the supervisor of the users’ researches.
- PATHDET cannot be used to diagnose, treat, prevent, or alleviate a disease or other condition in man or other animals.
- The users are allowed to use PATHDET for academic and non-profit purposes but not commercial purposes.
- Users’ personal information (e-mail address) is only used for the announcement of analysis submission and completion.
- PATHDET deletes the sequence reads immediately after completion of the analyses and does not use or provide the sequence data for any other purposes.
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