Version Compatibility

Reference examples tested with: 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.

Nanopore Basecalling

"Basecall my Nanopore data" → Convert raw electrical signal (FAST5/POD5) into nucleotide sequences with quality scores, optionally detecting modified bases.

• CLI: dorado basecaller sup pod5/ > calls.bam (recommended), dorado basecaller sup,5mCG_5hmCG pod5/ (with modifications)

Convert raw electrical signal from Nanopore sequencing into nucleotide sequences.

Dorado (Recommended)