Bioinformatics pipeline for shotgun metagenomic analysis of bacterial wilt-infected tomato rhizosphere soils (Kenya)

Pipeline v1.0 — Initial Release This repository contains the complete bioinformatics pipeline supporting the manuscript: Mogire et al. (2026). Metagenomic analysis of bacterial wilt-infected tomato rhizosphere microbiomes. (Manuscript under review) This shotgun metagenomic pipeline was developed for the analysis of rhizosphere soil samples from bacterial wilt-infected tomato farms across Kirinyaga, Kiambu, and Laikipia counties, Kenya. It covers the full workflow from raw read quality control through taxonomic classification, viral sequence confirmation, and Ralstonia-specific phage detection. Pipeline steps: Quality control of raw Illumina reads (FastQC) Metagenomic assembly (MEGAHIT / MetaSPAdes) Taxonomic classification (DIAMOND + MEGAN CE) Kraken2 viral classification with BLAST confirmation Ralstonia-specific phage detection Taxonomic abundance extraction at all levels BLAST-confirmed taxonomy summary for publication Associated data: Raw paired-end Illumina NovaSeq reads (2×150 bp) are deposited at NCBI SRA under BioProject accession PRJNA1273494. Dependencies: FastQC, MEGAHIT, MetaSPAdes, Kraken2, DIAMOND, MEGAN CE, BLAST+, seqtk