ottovon-dakurah/Cholera_genomics

This project seeks to understand the phylogeography of cholera out breaks in Africa and to find the virulence factors and resistant genes in these strains # Cholera Genomics Pipeline Overall, this is a reproducible, end-to-end Nextflow pipeline for cholera whole-genome sequence analysis, developed primarily for Vibrio cholerae but applicable to any bacterial pathogens.This project seeks to understand the phylogeography of cholera outbreaks in Africa and to find the virulence factors and resistant genes in the strains implicated in these outbreaks. ## Table of Contents - Overview - Pipeline steps - Requirements - Installation - Quick start - Input: samplesheet - Parameters - Output structure - Profiles - Running on HPC (SLURM) - Resuming a run - Skipping steps - Tools and containers - Citation - Contributing - License ## Overview This pipeline takes raw paired-end Illumina reads, SRA/ENA accessions, or pre-assembled contigs (or any mix of the three) and produces: - Per-sample QC reports - Trimmed reads - Core genome SNP alignment (via Snippy) - De novo assembled contigs (SPAdes) - MLST typing results - AMR and virulence gene profiles (ABRicate) - FastBAPS genomic clusters - Per-cluster recombination-masked alignments (Gubbins) - Parsimony-informative SNP alignment - Maximum-likelihood phylogenetic tree (IQ-TREE 3) - MultiQC summary report All tools run inside **Singularity/Apptainer/Docker** containers pulled from BioContainers, guaranteeing reproducibility across computing environments. ## Pipeline steps ``` Input (SRA, FASTQ, or contigs.fasta) │ ▼ 1. Download SRA reads (fasterq-dump / fastq-dump) [reads/SRA only] 2. Raw read QC (FastQC) [reads/SRA only] 3. Adapter trimming (fastp) [reads/SRA only] 4. Reference mapping (Snippy: read-based or --ctgs mode) 5. Core genome alignment (snippy-core) 6. De novo assembly (SPAdes) [reads/SRA only, contigs samples use their supplied assembly] 7. MLST typing (mlst) 8. AMR & virulence screening (ABRicate) 9 …