Release notes

Unreleased

metagraph build now chooses its default k-mer length at compile time from the alphabet’s packed 64-bit encoding, rounding down to an odd length for nucleotide alphabets:

• DNA/RNA: 31

• DNA5: 21

• Case-sensitive DNA: 15

• Protein: 12

To reproduce graphs built with the previous default, pass -k 3. Explicit -k values continue to override the default.

The workflow CLI now uses the selected MetaGraph executable’s build default instead of a separate default of 31. It records the resolved value in config.yaml and uses it throughout the build, including KMC stages. Pass -k 31 to retain the previous workflow default. When reusing a graph with --graph, its stored k-mer length is unchanged.