Version Compatibility

Reference examples tested with: 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.

Long-Read Alignment with minimap2

"Align my long reads to the reference" → Map ONT or PacBio reads using minimap2 with technology-specific presets for optimal sensitivity and accuracy.

• CLI: minimap2 -ax map-ont ref.fa reads.fq | samtools sort -o aligned.bam (ONT), minimap2 -ax map-hifi (PacBio HiFi)

Oxford Nanopore Alignment