Version Compatibility

Reference examples tested with: bcftools 1.19+, minimap2 2.26+, samtools 1.19+

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

• 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.

Medaka Polishing and Variant Calling

"Polish my ONT assembly with medaka" → Use neural networks trained on specific basecaller models to correct assembly errors and call variants from Nanopore data.

• CLI: medaka_polisher -i reads.fq -d draft.fa -o polished.fa -m r1041_e82_400bps_sup_v5.0.0

Basic Consensus Polishing