Version Compatibility

Reference examples tested with: BBTools 39.0+, Bowtie2 2.5.3+, FastQ Screen 0.15+, FastQC 0.12+, MultiQC 1.21+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Contamination Screening

Screen FASTQ files against multiple genomes to identify contamination sources using FastQ Screen.

"Check for contamination in sequencing data" → Align a sample of reads against multiple reference genomes to identify cross-species or cross-sample contamination.

• CLI: fastq_screen --conf fastq_screen.conf reads.fq

FastQ Screen Overview

FastQ Screen aligns a subset of reads against multiple reference genomes to identify:

• Cross-species contamination
• Bacterial/viral contamination
• Adapter sequences
• PhiX spike-in
• Sample swaps

Basic Usage

# Screen against configured genomes
fastq_screen sample.fastq.gz

# Multiple files
fastq_screen *.fastq.gz

# Specify output directory
fastq_screen --outdir qc_results/ sample.fastq.gz

# Custom config file
fastq_screen --conf my_screen.conf sample.fastq.gz

Configuration File

Create fastq_screen.conf:

# Database locations
DATABASE	Human	/path/to/human/genome
DATABASE	Mouse	/path/to/mouse/genome
DATABASE	Ecoli	/path/to/ecoli/genome
DATABASE	PhiX	/path/to/phix/genome
DATABASE	Adapters	/path/to/adapters
DATABASE	rRNA	/path/to/rrna

# Aligner (bowtie2 recommended)
BOWTIE2	/path/to/bowtie2

# Or use BWA
# BWA	/path/to/bwa

# Threads
THREADS	8

Pre-built Databases

# Download common screening databases
fastq_screen --get_genomes

# Downloads to ~/fastq_screen_databases/
# Includes: Human, Mouse, Rat, E.coli, PhiX, Adapters, etc.