Derleen123/Tomato-rhizosphere-metagenomics
Domain:
agricultureRecord type:
software
Creator:
Der
Host:
Bioinformatics pipeline for shotgun metagenomic analysis of bacterial wilt-infected tomato rhizosphere soils in Kenya. Includes quality control, assembly, taxonomic classification (Kraken2/DIAMOND/MEGAN), BLAST confirmation of viral sequences, and Ralstonia phage detection scripts.
# Metagenomic Analysis Pipeline
## Metagenomic Analysis of Bacterial-Wilt Tomato Rhizosphere Microbiomes
**Authors:** Derleen Mogire¹, Johnstone Neondo¹, Christabel Muhonja², Consolate Awuor², Daniel Mureithi², Stephen Ogada¹, Tofick Barasa Wekesa¹
**Affiliations:**
¹ Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
² Machakos University, Machakos, Kenya
**Corresponding author:** Derleen Mogire (contact via journal correspondence)
**Manuscript:** Mogire et al. (2026). Metagenomic analysis of bacterial-wilt tomato rhizosphere microbiomes (under review)
---
## Overview
This repository contains all bioinformatics scripts used for the shotgun metagenomic analysis of tomato rhizosphere soil samples from Kirinyaga, Kiambu, and Laikipia counties, Kenya (August–October 2022).
The pipeline covers:
1. Quality control of raw sequencing reads
2. Metagenomic assembly
3. Taxonomic classification (Kraken2 + DIAMOND/MEGAN)
4. BLAST confirmation of viral sequences
5. Ralstonia-specific phage detection
6. Taxonomic abundance extraction and summary
---
## Dependencies
| Tool | Version | Purpose |
|------|---------|---------|
| FastQC | ≥0.11.9 | Read quality control |
| MEGAHIT | 1.2.9 | Metagenomic assembly |
| MetaSPAdes | 3.15.5 | Alternative assembler |
| Kraken2 | ≥2.1.2 | Taxonomic classification |
| DIAMOND | ≥0.9.36 | Protein alignment |
| MEGAN | 6.24.20 | Taxonomic/functional classification |
| BLAST+ | ≥2.12 | Sequence confirmation |
| seqtk | ≥1.3 | Sequence extraction |
---
## Pipeline Structure
```
pipeline/
├── README.md # This file
├── 01_quality_control.sh # FastQC quality assessment
├── 02_assembly.sh # Metagenomic assembly (MEGAHIT/MetaSPAdes)
├── 03_taxonomic_classification.sh # DIAMOND + MEGAN classification
├── 04_kraken2_viral_blast.sh # Kraken2 viral classification + BLAST confirmation
├── 05_ralstonia_phage_de …
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