🧬 Thesis – Reproducible Genomic Analysis Pipeline (Nextflow)
This repository contains a reproducible bioinformatics pipeline developed for undergraduate thesis work. The pipeline performs genome processing and comparative analysis, including quality control, trimming, assembly, annotation, and pangenome analysis.
🚀 Features
Reproducible workflow using Nextflow
Modular pipeline design (DSL2)
Supports:
Quality Control (FastQC)
Trimming
Genome Assembly (SPAdes)
Genome Annotation (Prokka)
Comparative Genomics (MUMmer)
Pangenome Analysis (Roary)
Scalable and portable across systems
📦 Requirements
Make sure the following are installed:
Nextflow (>= 22.x) Conda (recommended)
⚙️ Setup
Clone the repository:
git clone https://github.com/realcann/Thesis.git
cd Thesis
📂 Input Data
The pipeline expects:
Paired-end FASTQ files
A reference genome in FASTA format
Example structure:
files/
├── sample_R1_001.fastq
├── sample_R2_001.fastq
└── Earth_reference.fasta
nextflow run main.nf -profile conda
--fastq_files "files/*_R{1,2}_001.fastq"
--ref_fasta "files/Earth_reference.fasta"
Custom output directory:
nextflow run main.nf -profile conda
--fastq_files "your_data/*_R{1,2}.fastq.gz"
--ref_fasta "your_data/reference.fasta"
--outdir "results"
📊 Output
Results will be generated in the specified output directory (out/ by default), including:
Quality control reports
Trimmed reads
Assembled genomes
Annotation outputs
Comparative analysis results
Pangenome outputs
🧪 Reproducibility
All dependencies are managed via environment.yml The pipeline can be executed on any system with Nextflow + Conda Intermediate files are stored in the work/ directory
📁 Project Structure
.
├── main.nf
├── nextflow.config
├── environment.yml
├── workflow/
├── modules/
├── files/ (not included)
├── out/ (generated)
👤 Author
Can Gerçek
Istanbul University
Molecular Biology and Genetics
Bioinformatics & Comparative Genomics
📌 Notes
This pipeline was developed as part of a thesis project focusing on reproducible genomic analysis.