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Eric Coissac
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- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
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SuperKmer and Minimizer-Based Sliding Window Analysis
This Go package provides functionality for extracting super k-mers from DNA sequences using a minimizer-based sliding window approach.
Core Concepts
- K-mers: Substrings of length
kfrom a DNA sequence. - Minimizer: The lexicographically smallest canonical m-mer (substring of length
m) among all(k − m + 1)overlapping m-mers in a given k-mer. - Super K-mer: A maximal contiguous subsequence where every consecutive k-mer shares the same minimizer.
Data Structures
SuperKmer
Represents a maximal region with uniform minimizer:
Minimizer: Canonical 64-bit hash of the shared m-mer.Start,End: Slice-style bounds (0-indexed, exclusive end).Sequence: Raw byte slice of the DNA subsequence.
dequeItem
Used internally to maintain a monotone deque:
position: Index of the m-mer in the sequence.canonical: Canonical hash value (e.g., lexicographically smallest of forward/reverse-complement).
Main Function
ExtractSuperKmers(seq, k, m, buffer)
- Extracts all maximal super k-mers from
seq. - Parameters validated:
1 ≤ m < k,2 ≤ k ≤ 31,- sequence length ≥
k.
- Uses an efficient O(n) time algorithm via internal iteration.
- Supports optional preallocation (
buffer) to reduce memory allocations.
Algorithm Highlights
- Maintains a sliding window of size
k − m + 1over m-mers. - Tracks the current minimizer using a monotone deque for O(1) updates per step.
- Detects minimizer transitions to delimit super k-mer boundaries.
Complexity
| Aspect | Bound |
|---|---|
| Time | O(n) (linear in sequence length) |
| Space | O(k − m + 1) for deque + output size |
Useful in genome compression, read clustering, and minimizer-based alignment acceleration.