Version Compatibility

Reference examples tested with: Cell Ranger 8.0+, FastQC 0.12+, GATK 4.5+, HISAT2 2.2.1+, MultiQC 1.21+, STAR 2.7.11+, Subread 2.0+, bcftools 1.19+, fastp 0.23+, kallisto 0.50+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Automated QC Reports with MultiQC

"Aggregate QC results into one report" → Combine outputs from FastQC, samtools, Picard, and other tools into a single interactive HTML report.

• CLI: multiqc . (scans current directory for recognized tool outputs)

Basic Usage