Leibniz International Proceedings in Informatics最新文献

{"title":"Bounding the Average Move Structure Query for Faster and Smaller RLBWT Permutations.","authors":"Nathaniel K Brown, Ben Langmead","doi":"10.4230/LIPIcs.SEA.2026.9","DOIUrl":"10.4230/LIPIcs.SEA.2026.9","url":null,"abstract":"<p><p>The <i>move structure</i> represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of Burrows-Wheeler Transform (BWT) runs, often applied in genomics. This is in thanks not only to theoretical improvements over past approaches, but great cache efficiency and average case query time in practice. This is true even without using the worst case guarantees provided by the interval splitting <i>balancing</i> of the original result. In this paper, we show that an even simpler type of splitting, <i>length capping</i> by truncating long intervals, bounds the average move structure query time to optimal whilst obtaining a superior construction time than the traditional approach. This also proves constant query time when amortized over a full traversal of a single cycle permutation from an arbitrary starting position. Such a scheme has surprising benefits both in theory and practice. For a move structure with <math><mi>r</mi></math> runs over a domain <math><mi>n</mi></math> , we replace all <math><mi>O</mi> <mo>(</mo> <mi>r</mi> <mspace></mspace> <mi>l</mi> <mi>o</mi> <mi>g</mi> <mspace></mspace> <mi>n</mi> <mo>)</mo></math> -bit components to reduce the overall representation by <math><mi>O</mi> <mo>(</mo> <mi>r</mi> <mspace></mspace> <mi>l</mi> <mi>o</mi> <mi>g</mi> <mspace></mspace> <mi>r</mi> <mo>)</mo></math> -bits. The worst case query time is also improved to <math><mi>O</mi> <mfenced><mrow><mi>l</mi> <mi>o</mi> <mi>g</mi> <mspace></mspace> <mfrac><mrow><mi>n</mi></mrow> <mrow><mi>r</mi></mrow> </mfrac> </mrow> </mfenced> </math> without balancing. An <math><mi>O</mi> <mo>(</mo> <mi>r</mi> <mo>)</mo></math> -time and space construction lets us apply the method to run-length encoded BWT (RLBWT) permutations such as LF and <math><mi>ϕ</mi></math> to obtain optimal-time algorithms for BWT inversion and suffix array (SA) enumeration in <math><mi>O</mi> <mo>(</mo> <mi>r</mi> <mo>)</mo></math> working space. Finally, we introduce the Orbit library, providing flexible plug and play move structure support, and use it to evaluate our splitting approach. Experiments find length capping construction is faster and uses less memory than balancing, and results in faster move structure queries: up to ~ 17 times faster when compared to an unbalanced representation of <math><mi>ϕ</mi></math> . We also see a space reduction in practice, with at least a ~ 40% disk size decrease for LF across large repetitive genomic collections when compared to a balanced/unbalanced move structure.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"371 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13523032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficiency of Learned Indexes on Genome Spectra.","authors":"Md Hasin Abrar, Paul Medvedev, Giorgio Vinciguerra","doi":"10.4230/LIPIcs.ESA.2025.18","DOIUrl":"10.4230/LIPIcs.ESA.2025.18","url":null,"abstract":"<p><p>Data structures on a multiset of genomic <math><mi>k</mi></math> -mers are at the heart of many bioinformatic tools. As genomic datasets grow in scale, the efficiency of these data structures increasingly depends on how well they leverage the inherent patterns in the data. One recent and effective approach is the use of learned indexes that approximate the rank function of a multiset using a piecewise linear function with very few segments. However, theoretical worst-case analysis struggles to predict the practical performance of these indexes. We address this limitation by developing a novel measure of piecewise-linear approximability of the data, called CaPLa (Canonical Piecewise Linear approximability). CaPLa builds on the empirical observation that a power-law model often serves as a reasonable proxy for piecewise linear-approximability, while explicitly accounting for deviations from a true power-law fit. We prove basic properties of CaPLa and present an efficient algorithm to compute it. We then demonstrate that CaPLa can accurately predict space bounds for data structures on real data. Empirically, we analyze over 500 genomes through the lens of CaPLa, revealing that it varies widely across the tree of life and even within individual genomes. Finally, we study the robustness of CaPLa as a measure and the factors that make genomic <math><mi>k</mi></math> -mer multisets different from random ones.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"351 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13073451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal Ensemble Logic for Integrative Representation of the Entirety of Clinical Trials.","authors":"Xiaojin Li, Yan Huang, Rashmie Abeysinghe, Zenan Sun, Hongyu Chen, Pengze Li, Xing He, Shiqiang Tao, Cui Tao, Jiang Bian, Licong Cui, Guo-Qiang Zhang","doi":"10.4230/LIPIcs.TIME.2025.13","DOIUrl":"10.4230/LIPIcs.TIME.2025.13","url":null,"abstract":"<p><p>Clinical trials are typically specified with protocols that define eligibility criteria, treatment regimens, follow-up schedules, and outcome assessments. Temporality is a hallmark of all clinical trials, reflected within and across trial components, with complex dependencies unfolding across multiple time points. Despite their importance, clinical trial protocols are described in free-text format, limiting their semantic precision and the ability to support automated reasoning, leverage data across studies and sites, or simulate trial execution under varying assumptions using Real-World Data. This paper introduces a formalized representation of clinical trials using Temporal Ensemble Logic (TEL). TEL incorporates metricized modal operators, such as \"always until <i>t</i>\" ( <math> <msub><mrow><mo>◻</mo></mrow> <mrow><mi>t</mi></mrow> </msub> </math> ) and \"possibly until <i>t</i>\" ( <math> <msub><mrow><mo>♢</mo></mrow> <mrow><mi>t</mi></mrow> </msub> </math> ), where <i>t</i> is a time-length parameter, to offer a logical framework for capturing phenotypes in biomedicine. TEL is more expressive in syntax than classical linear temporal logic (LTL) while maintaining the simplicity of semantic structures. The attributes of TEL are exploited in this paper to formally represent not only individual clinical trial components, but also the timing and sequential dependencies of these components as a whole. Modeling strategies and demonstration case studies are provided to show that TEL can represent the entirety of clinical trials, whereby providing a formal logical framework that can be used to represent the intricate temporal dependencies in trial structure specification. Since clinical trials are a cornerstone of evidence-based medicine, serving as the scientific basis for evaluating the safety, efficacy, and comparative effectiveness of therapeutic interventions, results reported here can serve as a stepping stone that leads to scalable, consistent, and reproducible representation and simulation of clinical trials across all disease domains.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"355 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12875094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards Passively Actuated Short-Range Telehaptics for Astronauts","authors":"Boguslavskiy, Matvey, Chappell, Digby, Nanayakkara, Thrishantha","doi":"10.4230/oasics.spacechi.2025.21","DOIUrl":"https://doi.org/10.4230/oasics.spacechi.2025.21","url":null,"abstract":"Human extra-vehicular activity (EVA) plays a vital role in current and near future space exploration for two reasons: the superior dexterity exhibited by human astronauts, and their flexible problem-solving and decision-making capabilities. However, the dexterity of astronauts during EVA is limited by the flexibility and tactility of their EVA suit gloves, which are primarily designed to provide thermal insulation and pressure for the hand. This creates a compromise between utility and protection. To address this compromise, a Passively Actuated Short-range Telehaptic (PAST) device is proposed. The PAST device couples the motion of fingers between a robotic hand and a human hand through a hydraulically actuated linkage. It also transfers tactile information, including pressure, direction of motion, and position of contact, via a taxel array. Results demonstrate that the proposed prototype PAST device surpasses an unpressurised benchmark heavy work glove (HWG) in tasks involving tactile position and motion direction identification. This provides evidence supporting the feasibility of enhancing astronaut dexterity during EVA through the use of PAST devices as an alternative paradigm to gloves.","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147381962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic classification with maximal exact matches in KATKA kernels and minimizer digests.","authors":"Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, Gonzalo Navarro","doi":"10.4230/LIPIcs.SEA.2024.10","DOIUrl":"10.4230/LIPIcs.SEA.2024.10","url":null,"abstract":"<p><p>For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular classifiers such as Kraken use <math><mi>k</mi></math> -mers, recent research indicates that using maximal exact matches (MEMs) can lead to better classifications. For example, we can ■ build an augmented FM-index over the the genomes in the tree concatenated in left-to-right order; ■ for each MEM in a read, find the interval in the suffix array containing the starting positions of that MEM's occurrences in those genomes; ■ find the minimum and maximum values stored in that interval; ■ take the lowest common ancestor (LCA) of the genomes containing the characters at those positions. This solution is practical, however, only when the total size of the genomes in the tree is fairly small. In this paper we consider applying the same solution to three lossily compressed representations of the genomes' concatenation: ■ a KATKA kernel, which discards characters that are not in the first or last occurrence of any <math> <mrow><msub><mi>k</mi> <mrow><mtext>max</mtext></mrow> </msub> </mrow> </math> -tuple, for a parameter <math> <mrow><msub><mi>k</mi> <mrow><mtext>max</mtext></mrow> </msub> </mrow> </math> ; a minimizer digest; ■ a KATKA kernel of a minimizer digest. With a test dataset and these three representations of it, simulated reads and various parameter settings, we checked how many reads' longest MEMs occurred only in the sequences from which those reads were generated (\"true positive\" reads). For some parameter settings we achieved significant compression while only slightly decreasing the true-positive rate.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"301 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141898483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PLA-index: A <i>k</i>-mer Index Exploiting Rank Curve Linearity.","authors":"Hasin Abrar, Paul Medvedev","doi":"10.4230/LIPIcs.WABI.2024.13","DOIUrl":"10.4230/LIPIcs.WABI.2024.13","url":null,"abstract":"<p><p>Given a sorted list of <i>k</i>-mers <i>S</i>, the rank curve of <i>S</i> is the function mapping a <i>k</i>-mer from the <i>k</i>-mer universe to the location in <i>S</i> where it either first appears or would be inserted. An exciting recent development is the observation that, for certain datasets, the rank curve is predictable and can be exploited to create small search indices. In this paper, we develop a novel search index that first estimates a <i>k</i>-mer's rank using a piece-wise linear approximation of the rank curve and then does a local search to determine the precise location of the <i>k</i>-mer in the list. We combine ideas from previous approaches and supplement them with an innovative data representation strategy that substantially reduces space usage. Our PLA-index uses an order of magnitude less space than Sapling and uses less than half the space of the PGM-index, for roughly the same query time. For example, using only 9 MiB of memory, it can narrow down the position of <i>k</i>-mer in the suffix array of the human genome to within 255 positions. Furthermore, we demonstrate the potential of our approach to impact a variety of downstream applications. First, the PLA-index halves the time of binary search on the suffix array of the human genome. Second, the PLA-index reduces the space of a direct-access lookup table by 76 percent, without increasing the run time. Third, we plug the PLA-index into a state-of-the-art read aligner Strobealign and replace a 2 GiB component with a PLA-index of size 1.5 MiB, without significantly effecting runtime. The software and reproducibility information is freely available at https://github.com/medvedevgroup/pla-index.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"312 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12037174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Applying the Safe-And-Complete Framework to Practical Genome Assembly.","authors":"Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I Tomescu","doi":"10.4230/LIPIcs.WABI.2024.8","DOIUrl":"10.4230/LIPIcs.WABI.2024.8","url":null,"abstract":"<p><p>Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the <i>omnitig algorithm</i>, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (<i>simple omnitigs</i>), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the <i>D. melanogaster</i> and the <i>C. elegans</i> genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"312 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12037172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143986151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.","authors":"Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, Mingfu Shao","doi":"10.4230/LIPIcs.WABI.2024.22","DOIUrl":"10.4230/LIPIcs.WABI.2024.22","url":null,"abstract":"<p><p>Modern sequencing technologies allow for the addition of short-sequence tags, known as anchors, to both ends of a captured molecule. Anchors are useful in assembling the full-length sequence of a captured molecule as they can be used to accurately determine the endpoints. One representative of such anchor-enabled technology is LoopSeq Solo, a synthetic long read (SLR) sequencing protocol. LoopSeq Solo also achieves ultra-high sequencing depth and high purity of short reads covering the entire captured molecule. Despite the availability of many assembly methods, constructing full-length sequence from these anchor-enabled, ultra-high coverage sequencing data remains challenging due to the complexity of the underlying assembly graphs and the lack of specific algorithms leveraging anchors. We present Anchorage, a novel assembler that performs anchor-guided assembly for ultra-high-depth sequencing data. Anchorage starts with a kmer-based approach for precise estimation of molecule lengths. It then formulates the assembly problem as finding an optimal path that connects the two nodes determined by anchors in the underlying compact de Bruijn graph. The optimality is defined as maximizing the weight of the smallest node while matching the estimated sequence length. Anchorage uses a modified dynamic programming algorithm to efficiently find the optimal path. Through both simulations and real data, we show that Anchorage outperforms existing assembly methods, particularly in the presence of sequencing artifacts. Anchorage fills the gap in assembling anchor-enabled data. We anticipate its broad use as anchor-enabled sequencing technologies become prevalent. Anchorage is freely available at https://github.com/Shao-Group/anchorage; the scripts and documents that can reproduce all experiments in this manuscript are available at https://github.com/Shao-Group/anchorage-test.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"312 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142956038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exact Sketch-Based Read Mapping.","authors":"Tizian Schulz, Paul Medvedev","doi":"10.4230/LIPIcs.WABI.2023.14","DOIUrl":"10.4230/LIPIcs.WABI.2023.14","url":null,"abstract":"<p><p>Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a \"similar sequence\". Traditionally, \"similar sequence\" was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold. In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in <math><mi>𝒪</mi> <mfenced><mrow><mo>|</mo> <mi>t</mi> <mo>|</mo> <mo>+</mo> <mo>|</mo> <mi>p</mi> <mo>|</mo> <mo>+</mo> <msup><mrow><mo>ℓ</mo></mrow> <mrow><mn>2</mn></mrow> </msup> </mrow> </mfenced> </math> time and <math><mi>Θ</mi> <mfenced> <mrow> <msup><mrow><mo>ℓ</mo></mrow> <mrow><mn>2</mn></mrow> </msup> </mrow> </mfenced> </math> space, where <math><mo>|</mo> <mi>t</mi> <mo>|</mo></math> is the number of <math><mi>k</mi></math> -mers inside the sketch of the reference, <math><mo>|</mo> <mi>p</mi> <mo>|</mo></math> is the number of <math><mi>k</mi></math> -mers inside the read's sketch and <math><mo>ℓ</mo></math> is the number of times that <math><mi>k</mi></math> -mers from the pattern sketch occur in the sketch of the text. We evaluate our algorithm's performance in mapping long reads to the T2T assembly of human chromosome Y, where ampliconic regions make it desirable to find all good mapping positions. For an equivalent level of precision as minimap2, the recall of our algorithm is 0.88, compared to only 0.76 of minimap2.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"273 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11146199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141238322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compression Algorithm for Colored de Bruijn Graphs.","authors":"Amatur Rahman, Yoann Dufresne, Paul Medvedev","doi":"10.4230/LIPIcs.WABI.2023.17","DOIUrl":"10.4230/LIPIcs.WABI.2023.17","url":null,"abstract":"<p><p>A colored de Bruijn graph (also called a set of k-mer sets), is a set of k-mers with every k-mer assigned a set of colors. Colored de Bruijn graphs are used in a variety of applications, including variant calling, genome assembly, and database search. However, their size has posed a scalability challenge to algorithm developers and users. There have been numerous indexing data structures proposed that allow to store the graph compactly while supporting fast query operations. However, disk compression algorithms, which do not need to support queries on the compressed data and can thus be more space-efficient, have received little attention. The dearth of specialized compression tools has been a detriment to tool developers, tool users, and reproducibility efforts. In this paper, we develop a new tool that compresses colored de Bruijn graphs to disk, building on previous ideas for compression of k-mer sets and indexing colored de Bruijn graphs. We test our tool, called ESS-color, on various datasets, including both sequencing data and whole genomes. ESS-color achieves better compression than all evaluated tools and all datasets, with no other tool able to consistently achieve less than 44% space overhead.</p>","PeriodicalId":30209,"journal":{"name":"Leibniz International Proceedings in Informatics","volume":"273 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11071130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}