FastQ Screen quickly identifies contamination by aligning a subset of reads against multiple reference genomes. It detects cross-species contamination, bacterial contamination, adapter sequences, and sample swaps.
conda install -c bioconda fastq-screen
# Download pre-built databases
fastq_screen --get_genomesTell your AI agent what you want to do:
- "Screen my FASTQ files for contamination"
- "Check if my human sample has any mouse contamination"
- "Verify my samples are not swapped"
"Run FastQ Screen on my samples to check for contamination"
"Screen my FASTQ files against human, mouse, and common contaminants"
"My RNA-seq has unexpected results, check for contamination or sample swap"
"Identify the source of contamination in my samples"
"Set up FastQ Screen with custom genome databases"
"Add E. coli and yeast to my contamination screening panel"
- Configure FastQ Screen with appropriate reference databases
- Run screening on a subset of reads from each sample
- Generate reports showing percentage mapping to each genome
- Identify problematic samples with contamination or swaps
- Recommend appropriate remediation steps
Genome %One_hit %Multi_hit
Human 95.0 2.0
Mouse 0.1 0.0
Ecoli 0.0 0.0
Adapters 0.1 0.0
| Issue | Pattern | Solution |
|---|---|---|
| Bacterial contamination | High E.coli/bacteria % | Investigate source |
| Sample swap | Wrong species dominant | Re-sequence or exclude |
| Adapter contamination | High Adapters % | Run adapter trimming |
| PhiX spike-in | High PhiX % | Filter PhiX reads |
| rRNA contamination | High rRNA % | rRNA depletion failed |
- Run contamination screening early before investing in alignment and analysis
- Include common contaminants: E. coli, yeast, PhiX, adapters
- For xenograft samples, expect mixed human/mouse signal
- Sample swaps are easier to detect than fix - verify sample identity early
- Use
--subsetto screen a random subset of reads for faster results