Version Compatibility

Reference examples tested with: pandas 2.2+, 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.

UMI Processing

"Deduplicate reads using UMIs" → Extract UMI barcodes, group reads by UMI+position, and collapse PCR duplicates to count unique molecules.

• CLI: umi_tools extract + umi_tools dedup (UMI-tools)
• CLI: fgbio GroupReadsByUmi + fgbio CallMolecularConsensusReads

UMIs (Unique Molecular Identifiers) are short random sequences added during library preparation to tag individual molecules before PCR amplification. This enables accurate PCR duplicate removal and molecule counting.