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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Research Project #447533
Research Project: Implementation of a Computational Pipeline for Detection of Viruses Using High Throughput Sequence Data

Location: Horticultural Crops Disease and Pest Management Research Unit

Project Number: 2072-22000-046-065-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2026
End Date: Jul 31, 2028

Objective:
To implement a computational pipeline for detection of viruses in the Clean Plant Program using high throughput sequence data.

Approach:
We will adapt the open source PhytoPipe bioinformatics pipeline used by APHIS for plant pathogen detection using RNA-seq data to operate in within the framework of the PathogenSurvelliance pipeline using the nexflow environment. This will expand the PathogenSuveillance pipeline to encompass all plant pathogens. We will use high-throughput sequencing (HTS) data processed by USDA ARS HCDPMRU in Corvallis for diagnosis at Oregon State using the PhytoPipe implementation. The pipeline will be implemented in the SCINet high performance computing cluster of USDA ARS.