Klebsiella pneumoniae SNP calling & drug resistance annotation pipeline

This pipeline is a bash script that automates quality control, variant calling, and drug resistance gene annotation for Klebsiella pneumoniae whole-genome sequencing data. It leverages tools such as FastQC, MultiQC, and Snippy to perform SNP calling and identify mutations associated with antibiotic resistance.

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Features

• Performs quality checks using FastQC
• Generates combined quality reports using MultiQC
• Calls SNPs using Snippy with a reference genome
• Detects and annotates drug resistance mutations
• Outputs drug-specific resistance summaries per sample

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Input requirements

1. A list.txt file with one sample name per line (without file extensions).

2. Paired-end FASTQ files for each sample named as:

   • sample_1.fastq.gz
   • sample_2.fastq.gz

3. A GenBank reference file for Klebsiella pneumoniae (update the path in the script).

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How to run

1. Make the script executable:

chmod +x klebsiella_pipeline.sh

2. Run the script from within your working directory:

./klebsiella_pipeline.sh

Ensure the script is located in the same directory as your FASTQ files and list.txt.

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Output files

For each sample, the script generates:

• sample.snps/ directory containing SNP calling output
• sample.Drug-Resistance-Details.txt: Detected resistance mutations
• Drug-specific summaries such as:
  • sample.Aminoglycoside.Resistance.txt
  • sample.Beta-lactam.Resistance.txt
  • sample.Fluoroquinolone.Resistance.txt, etc.

Empty files are automatically removed to declutter the output.

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Resistance genes detected

Drug class	Genes detected
Aminoglycosides	aacA4, rmtC
Beta-lactams	bla
Chloramphenicol	ramR
Fluoroquinolones	ramR, oqxA, oqxB, gyrA, parC
Fosfomycin	fosA
Polymyxins	mgrB
Sulfonamides	sul1
Tetracyclines	tet
Macrolides	mph

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Quote to remember

"Bioinformatics is not something you are taught, it’s a way of life."

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📧 Email:

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License

This script is provided under the MIT License.