Table of Contents
Super-kmers
A super-kmer is a maximal run of consecutive, overlapping kmers from a read that share the same canonical minimizer (see Minimizer selection). Each kmer in the run overlaps the next by k-1 nucleotides. A super-kmer is capped at 256 nucleotides; a longer run is split at that boundary.
For a random minimizer of length m over kmers of length k, the expected length of a super-kmer is approximately (Golan & Shur 2025; Zheng et al. 2020):
L_{\text{nt}} \approx \frac{k-m+2}{2} + k - 1
For k=31, m=13 this is about 40 nucleotides; in practice super-kmers rarely exceed a few dozen nucleotides.
Canonical super-kmers
A canonical super-kmer is the canonical form of a super-kmer (see DNA encoding): the lexicographic minimum of the super-kmer and its reverse complement. When a read and its reverse complement are both encountered, they produce super-kmers that are reverse complements of each other; both reduce to the same canonical super-kmer, so a genomic region is represented once regardless of which strand was read.
Super-kmers are the unit of work used throughout construction and querying: sequences are decomposed into super-kmers first, and every downstream step (partition routing, deduplication, counting) operates on them rather than on individual kmers.
Bibliography
Golan, S. & Shur, A.M. (2025). Expected density of random minimizers. In: Lecture Notes in Computer Science, Lecture Notes in Computer Science. Springer Nature Switzerland, Cham, pp. 347–360.
Zheng, H., Kingsford, C. & Marçais, G. (2020). Improved design and analysis of practical minimizers. Bioinformatics (Oxford, England), 36, i119–i127.
Wiki sidebar
Theory
Kmer indexing
- DNA encoding
- Kmers
- Minimizer selection
- Super-kmers
- Partitioning and indexing architecture
- Low-complexity kmer filter
Phylogeny
Kmer-based
SNP-based
Usage
- superkmer
- index
- merge
- filter
- select
- query
- dump
- annotate
- phylo
- unitig
- estimate
- convert
- utils
- pack
- Predicates and taxonomy paths