Version Compatibility

Reference examples tested with: matplotlib 3.8+, numpy 1.26+, picard 3.1+, pysam 0.22+, samtools 1.19+

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.

Alignment Validation

Post-alignment quality control to verify alignment quality and identify issues.

"Check alignment quality" → Compute post-alignment QC metrics (mapping rate, pairing, insert size, strand balance) to identify issues before downstream analysis.

• CLI: samtools flagstat, samtools stats, Picard CollectAlignmentSummaryMetrics
• Python: pysam.AlignmentFile iteration with metric calculations