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Quick Start

Get up and running with BactScout in 5 minutes.

1. Install BactScout

git clone https://github.com/ghruproject/bactscout.git
cd bactscout
pixi install

2. Prepare Your Input

Organize your FASTQ files in a directory with standard naming:

data/
├── sample_001_R1.fastq.gz
├── sample_001_R2.fastq.gz
├── sample_002_R1.fastq.gz
├── sample_002_R2.fastq.gz
└── ...

Naming Formats Supported

  • sample_001_R1.fastq.gz ✅
  • sample_001_1.fastq.gz ✅
  • sample_001.fastq ✅
  • sample.001_R1.fq.gz ✅

3. Run Quality Control

pixi run bactscout qc data/ -o results/

pixi run bactscout collect data/sample_001_R1.fastq.gz data/sample_001_R2.fastq.gz -o results/

4. Generate Summary Report

pixi run bactscout summary results/

This creates results/final_summary.csv with all samples merged.

5. Analyze Results

Check results/final_summary.csv:

sample_id,a_final_status,coverage_status,mlst_status,species,...
sample_001,PASSED,PASSED,PASSED,Escherichia coli,...
sample_002,WARNING,PASSED,WARNING,Salmonella enterica,...

Common Options

# Use custom configuration
pixi run bactscout qc data/ -c custom_config.yml

# Specify number of threads
pixi run bactscout qc data/ -t 8

# Skip preflight checks (not recommended)
pixi run bactscout qc data/ --skip-preflight

What's Next?