Contamination Detection

CheckM2 (Recommended)

# Run CheckM2 on single genome
checkm2 predict --input assembly.fa --output-directory checkm2_output --threads 16

# Run on multiple genomes (directory of FASTAs)
checkm2 predict --input genomes/ --output-directory checkm2_output \
    --threads 16 --extension fa

# Output: quality_report.tsv with Completeness, Contamination, Coding_Density

Interpret CheckM2 Results