PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.

ABSTRACT:

Background

Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-throughput sequencing (HTS) has been applied successfully for plant pathogen discovery, leading to its current application in routine pathogen detection. However, the analysis of massive amounts of HTS data has become one of the major challenges for the use of HTS more broadly as a rapid diagnostics tool. Several bioinformatics pipelines have been developed to handle HTS data with a focus on plant virus and viroid detection. However, there is a need for an integrative tool that can simultaneously detect a wider range of other plant pathogens in HTS data, such as bacteri

SUBMITTER: Hu X 

PROVIDER: S-EPMC10717670 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature