WGS Bacteria Analysis Pipeline

This repository contains scripts and a Nextflow workflow for performing Whole Genome Sequencing (WGS) Antimicrobial Resistance (AMR) analysis. it is designed to process raw illumina sequencing reads, perform quality assessment using FastQC, MultiQC, fastp/Trimmomatic, trim low-quality bases and adapter sequences, and produce high-quality reads ready for downstream analses.

Pipeline Overview

The workflow performs:

• Quality control on raw sequencing reads
• Genome assembly
• AMR gene detection
• Post-processing and reporting

The pipeline is designed to handle multiple samples and can work with Illumina or Oxford Nanopore sequencing data.

Repository Contents

• amr_nextflow_pipeline/ : Nextflow workflow and configuration files
• *.sh scripts : Auxiliary scripts for various steps in the pipeline, including:
  • assembly.sh : Controls genome assembly using tools like SPAdes and Flye
  • flye.sh : Runs Flye assembler specifically for long-read assemblies
  • spade.sh / spades.sh / : Runs SPAdes assembler for short-read assemblies
  • unicycler.sh / ONTunicycler.sh : Hybrid assembly using Unicycler
  • genome_qc.sh / quast.sh : Performs assembly quality control with QUAST
  • is_finder.sh : Identifies insertion sequences in assembled genomes
  • intergron.sh / abricate_interon.sh : Detects integrons and antimicrobial resistance genes using ABRicate and integron detection
  • trimmed.sh : Performs read trimming and quality control using fastp or Trimmomatic
• .gitignore : Ignores runtime and temporary files

Requirements

• Nextflow
• Linux environment recommended
• Conda or Docker for managing dependencies

How to Run

From the amr_nextflow_pipeline/ directory:

./run_pipeline.sh
# or run directly using Nextflow
nextflow run amr_pipeline2.nf -c nextflow.config