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Complement Submodular Information Measures for Balanced and Robust Data Selection A Proof of a Conjecture on Positive and Negative Square Energies of Unicyclic Graphs Laplacian Spectrum of the Weakly Zero-Divisor Graph of a Finite Commutative Ring An identity for second Eulerian numbers via lattice-point counting $t$-tone edge coloring of graphs Constructing Maximal Bumpless Pipedreams for Double Grothendieck Polynomials Mubayi's Polynomial-Ideal Conjecture and Cover-Ideal Turán Methods Implicit Binarization via Complex Phase Dynamics in Combinatorial Optimization The limits of Schur multipliers in Pólya conversion problems for the $q$-permanent function Universality theorems for generalized splines Framing Triangulations for Arbitrary Integer Flow Polytopes On the Common Generalization of Gentle Algebras and Framed Directed Acyclic Graphs The complexity of frugal digraph homomorphisms Chaotic and periodic behavior of jeu de taquin on infinite Young tableaux Enumerating Pattern Avoiding Parking Functions Incidence toric ideals and three-point functions Unique Winning Opening Move in Three-Row Chomp Strong majority colorings of graphs A Balancing Theorem for Spanning Trees of Rectangular Grid Graphs Spectral radius and edge-disjoint connected factors of graphs New invariants for rank metric codes, with applications to the classification of rank two semifields of order 256 Flexible DP-4-coloring of planar graphs without 4-cycles and intersecting triangles Balanced intersection size distributions in projective planes List Reconstruction Problem with List Size Two Is Dimensionality a Barrier for Retrieval Models? The INIEP: Irreducible and Positive Realizations The number of Pfaffian orientations on punctured polygonally cellulated surfaces Explicit Construction of Polytopes whose Ehrhart Polynomials Realize any Given Sign Pattern Finite-state enumeration of adjacency-constrained 132-avoiding permutations AMDS and quantum AMDS Constacyclic codes of length $4p^ς$ over $\mathbb{F}_{{p}^{m}}$
Efficient k-mer Dataset Compression Using Eulerian Covers...
H. Z. Q. Chen, S. Kitaev, X. Lang, A. Pyatkin, R. Tang · 2025-10-26 · via math.CO updates on arXiv.org

Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for lossless compression of the k-mer multiset. Our core method achieves a minimal text representation (W) by computing an optimal Eulerian cover (minimum string count) of the dataset's de Bruijn graph, enabled by an efficient local Eulerization technique. The resulting strings are then further compressed losslessly using the Burrows-Wheeler Transform (BWT). Leveraging de Bruijn graph properties, MCTR is proven to achieve linear time and space complexity and guarantees complete reconstruction of the original k-mer multiset, including frequencies. Using simulated and real genomic data, we evaluated MCTR's performance (list and frequency representations) against the state-of-the-art lossy unitigging tool greedytigs (from matchtigs). We measured core execution time and the raw compression ratio cmpr = weight(M)/weight(W), where M is the input sequence data). Benchmarks confirmed MCTR's data fidelity but revealed performance trade-offs inherent to lossless representation. GreedyTigs was significantly faster. Regarding raw compression, GreedyTigs achieved high ratios (cmpr approx 14) on noisy real data for its lossy sequence output. On real data, MCTR (frequency) showed moderate raw compression (cmpr approx 1.5-2.7), while MCTR (list) showed none (cmpr approx 1). Importantly, the full MCTR+BWT pipeline significantly outperforms BWT alone for enhanced lossless compression. Our results establish MCTR as a valuable, theoretically grounded tool for applications demanding efficient, lossless storage and analysis of k-mer multisets, complementing lossy methods optimized for sequence summarization.