Fig. 1
From: PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Flowchart describing processes and steps performed by the PhytoPipe workflow. The pipeline integrates reads preprocessing (A), reads classification (B), assembly-based annotation (C), and reference-based mapping (D) into a single workflow. The entire protocol can be run starting from raw sequence data in the form of single- or paired-end FASTQ files. The results are summarized in an HTML report file, tables, and Krona plots for an expert interpretation