{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:00:11Z","timestamp":1785423611117,"version":"3.56.0"},"posted":{"date-parts":[[2025,11,26]]},"group-title":"Bioinformatics","reference-count":116,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T00:00:00Z","timestamp":1764115200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R01AI183668"],"award-info":[{"award-number":["R01AI183668"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01HD106017"],"award-info":[{"award-number":["R01HD106017"]}],"id":[{"id":"https:\/\/ror.org\/04byxyr05","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,11,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.<\/jats:p>","DOI":"10.1101\/2025.11.24.690211","type":"posted-content","created":{"date-parts":[[2025,11,26]],"date-time":"2025-11-26T23:50:15Z","timestamp":1764201015000},"source":"Crossref","is-referenced-by-count":0,"title":["Comparative metagenomics using pan-metagenomic graphs"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4697-6079","authenticated-orcid":false,"given":"Izaak","family":"Coleman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalya","family":"Mametyarova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7165-2669","authenticated-orcid":false,"given":"Andrey","family":"Zaznaev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4774-4392","authenticated-orcid":false,"given":"Peiwen","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoli","family":"Meydan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0044-7617","authenticated-orcid":false,"given":"Aviya","family":"Litman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayushi","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lily","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-5352-5407","authenticated-orcid":false,"given":"Amanda","family":"Simkhovich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dwayne","family":"Seeram","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5815-9717","authenticated-orcid":false,"given":"Heekuk","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5759-3730","authenticated-orcid":false,"given":"Yael R.","family":"Nobel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2085-126X","authenticated-orcid":false,"given":"Aya Brown","family":"Kav","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6128-7231","authenticated-orcid":false,"given":"Itsik","family":"Pe\u2019er","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9798-4768","authenticated-orcid":false,"given":"Anne-Catrin","family":"Uhlemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0609-0858","authenticated-orcid":false,"given":"Tal","family":"Korem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025112801450436000_2025.11.24.690211v1.1","doi-asserted-by":"crossref","unstructured":"Navarro-Garcia, F . (2015). Escherichia coli O104:H4 Pathogenesis: An Enteroaggregative E. coli\/Shiga Toxin-Producing E. coli Explosive Cocktail of High Virulence. In Enterohemorrhagic Escherichia coli and Other Shiga Toxin-Producing E. coli (American Society of Microbiology), pp. 533\u2013539.","DOI":"10.1128\/9781555818791.ch26"},{"key":"2025112801450436000_2025.11.24.690211v1.2","doi-asserted-by":"crossref","first-page":"dlab092","DOI":"10.1093\/jacamr\/dlab092","article-title":"Extended-spectrum \u03b2-lactamases: an update on their characteristics, epidemiology and detection","volume":"3","year":"2021","journal-title":"JAC Antimicrob. Resist"},{"key":"2025112801450436000_2025.11.24.690211v1.3","doi-asserted-by":"publisher","DOI":"10.1007\/s10142-006-0027-2"},{"key":"2025112801450436000_2025.11.24.690211v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2008.09.006"},{"key":"2025112801450436000_2025.11.24.690211v1.5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003788"},{"key":"2025112801450436000_2025.11.24.690211v1.6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0030231"},{"key":"2025112801450436000_2025.11.24.690211v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00690-07"},{"key":"2025112801450436000_2025.11.24.690211v1.8","doi-asserted-by":"publisher","DOI":"10.1126\/science.1160354"},{"key":"2025112801450436000_2025.11.24.690211v1.9","first-page":"e0081621","article-title":"Embracing Metagenomic Complexity with a Genome-Free Approach","volume":"6","year":"2021","journal-title":"mSystems"},{"key":"2025112801450436000_2025.11.24.690211v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2013.12.019"},{"key":"2025112801450436000_2025.11.24.690211v1.11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0906217106"},{"key":"2025112801450436000_2025.11.24.690211v1.12","doi-asserted-by":"publisher","DOI":"10.1126\/science.aau6323"},{"key":"2025112801450436000_2025.11.24.690211v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-40719-7"},{"key":"2025112801450436000_2025.11.24.690211v1.14","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciy199"},{"key":"2025112801450436000_2025.11.24.690211v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.03.007"},{"key":"2025112801450436000_2025.11.24.690211v1.16","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.chom.2025.04.010","article-title":"Intraspecies dynamics underlie the apparent stability of two important skin microbiome species","volume":"33","year":"2025","journal-title":"Cell Host Microbe"},{"key":"2025112801450436000_2025.11.24.690211v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1065-y"},{"key":"2025112801450436000_2025.11.24.690211v1.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.12.038"},{"key":"2025112801450436000_2025.11.24.690211v1.19","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.10.022"},{"key":"2025112801450436000_2025.11.24.690211v1.20","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1186\/s12859-019-3301-8","article-title":"LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics","volume":"20","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2025112801450436000_2025.11.24.690211v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0718-6"},{"key":"2025112801450436000_2025.11.24.690211v1.22","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","year":"2017","journal-title":"Nat. Microbiol"},{"key":"2025112801450436000_2025.11.24.690211v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/J.CELL.2019.01.001\/ATTACHMENT\/31D7FB71-DCA8-4659-BC04-FB25BCC69750\/MMC7.XLSX"},{"key":"2025112801450436000_2025.11.24.690211v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-0965"},{"key":"2025112801450436000_2025.11.24.690211v1.25","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214155.116"},{"key":"2025112801450436000_2025.11.24.690211v1.26","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.85302"},{"key":"2025112801450436000_2025.11.24.690211v1.27","doi-asserted-by":"publisher","DOI":"10.1101\/2024.02.09.579496"},{"key":"2025112801450436000_2025.11.24.690211v1.28","doi-asserted-by":"crossref","first-page":"375","DOI":"10.3390\/microorganisms12020375","article-title":"The Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov","volume":"12","year":"2024","journal-title":"Microorganisms"},{"key":"2025112801450436000_2025.11.24.690211v1.29","doi-asserted-by":"publisher","DOI":"10.1101\/2025.03.16.643550"},{"key":"2025112801450436000_2025.11.24.690211v1.30","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-022-04601-8"},{"key":"2025112801450436000_2025.11.24.690211v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-05896-x"},{"key":"2025112801450436000_2025.11.24.690211v1.32","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10876-0"},{"key":"2025112801450436000_2025.11.24.690211v1.33","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02168-z"},{"key":"2025112801450436000_2025.11.24.690211v1.34","first-page":"mgen001034","article-title":"PanGraph: scalable bacterial pan-genome graph construction","volume":"9","year":"2023","journal-title":"Microb Genom"},{"key":"2025112801450436000_2025.11.24.690211v1.35","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1791-3"},{"key":"2025112801450436000_2025.11.24.690211v1.36","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00619-08"},{"key":"2025112801450436000_2025.11.24.690211v1.37","doi-asserted-by":"crossref","first-page":"4379","DOI":"10.1038\/s41467-020-18164-7","article-title":"Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C","volume":"11","year":"2020","journal-title":"Nat. Commun"},{"key":"2025112801450436000_2025.11.24.690211v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/nature18927"},{"key":"2025112801450436000_2025.11.24.690211v1.39","doi-asserted-by":"publisher","DOI":"10.1038\/nature10571"},{"key":"2025112801450436000_2025.11.24.690211v1.40","doi-asserted-by":"crossref","first-page":"10689","DOI":"10.1038\/s41598-020-67416-5","article-title":"Terabase-scale metagenome coassembly with MetaHipMer","volume":"10","year":"2020","journal-title":"Sci. Rep"},{"key":"2025112801450436000_2025.11.24.690211v1.41","doi-asserted-by":"crossref","first-page":"e0143421","DOI":"10.1128\/Spectrum.01434-21","article-title":"Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes","volume":"9","year":"2021","journal-title":"Microbiol Spectr"},{"key":"2025112801450436000_2025.11.24.690211v1.42","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01259-2"},{"key":"2025112801450436000_2025.11.24.690211v1.43","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.126"},{"key":"2025112801450436000_2025.11.24.690211v1.44","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1058-x"},{"key":"2025112801450436000_2025.11.24.690211v1.45","doi-asserted-by":"crossref","first-page":"3208","DOI":"10.1016\/j.csbj.2022.06.019","article-title":"KOMB: K-core based de novo characterization of copy number variation in microbiomes","volume":"20","year":"2022","journal-title":"Comput. Struct. Biotechnol. J"},{"key":"2025112801450436000_2025.11.24.690211v1.46","first-page":"506","article-title":"KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome","volume":"29","year":"2024","journal-title":"Pac. Symp. Biocomput"},{"key":"2025112801450436000_2025.11.24.690211v1.47","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.2403.01610"},{"key":"2025112801450436000_2025.11.24.690211v1.48","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1186\/s13059-020-02066-4","article-title":"Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity","volume":"21","year":"2020","journal-title":"Genome Biol"},{"key":"2025112801450436000_2025.11.24.690211v1.49","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw312"},{"key":"2025112801450436000_2025.11.24.690211v1.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12633-4"},{"key":"2025112801450436000_2025.11.24.690211v1.51","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0603-3"},{"key":"2025112801450436000_2025.11.24.690211v1.52","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-019-0633-6"},{"key":"2025112801450436000_2025.11.24.690211v1.53","doi-asserted-by":"publisher","DOI":"10.1101\/2022.06.30.498290"},{"key":"2025112801450436000_2025.11.24.690211v1.54","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"2025112801450436000_2025.11.24.690211v1.55","doi-asserted-by":"publisher","DOI":"10.1101\/gr.213959.116"},{"key":"2025112801450436000_2025.11.24.690211v1.56","first-page":"000794","article-title":"Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data","volume":"8","year":"2022","journal-title":"Microb. Genom"},{"key":"2025112801450436000_2025.11.24.690211v1.57","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty093"},{"key":"2025112801450436000_2025.11.24.690211v1.58","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.03.006"},{"key":"2025112801450436000_2025.11.24.690211v1.59","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2015-309800"},{"key":"2025112801450436000_2025.11.24.690211v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0450-2"},{"key":"2025112801450436000_2025.11.24.690211v1.61","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-022-01410-z"},{"key":"2025112801450436000_2025.11.24.690211v1.62","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.65088"},{"key":"2025112801450436000_2025.11.24.690211v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0405-7"},{"key":"2025112801450436000_2025.11.24.690211v1.64","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-019-0406-6"},{"key":"2025112801450436000_2025.11.24.690211v1.65","doi-asserted-by":"publisher","DOI":"10.1111\/j.1442-9993.2001.01070.pp.x)"},{"key":"2025112801450436000_2025.11.24.690211v1.66","doi-asserted-by":"publisher","DOI":"10.1007\/s00134-018-5268-8"},{"key":"2025112801450436000_2025.11.24.690211v1.67","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0186195"},{"key":"2025112801450436000_2025.11.24.690211v1.68","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-024-01054-w"},{"key":"2025112801450436000_2025.11.24.690211v1.69","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.suppl_1.S294"},{"key":"2025112801450436000_2025.11.24.690211v1.70","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1011071"},{"key":"2025112801450436000_2025.11.24.690211v1.71","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1112"},{"key":"2025112801450436000_2025.11.24.690211v1.72","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01953-y"},{"key":"2025112801450436000_2025.11.24.690211v1.73","first-page":"388","article-title":"Gene and domain shuffling in lytic cassettes of Enterococcus spp. bacteriophages","volume":"13","year":"2023","journal-title":"Biotech"},{"key":"2025112801450436000_2025.11.24.690211v1.74","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.00950"},{"key":"2025112801450436000_2025.11.24.690211v1.75","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.70.10.5810-5817.2004"},{"key":"2025112801450436000_2025.11.24.690211v1.76","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.66.4.1654-1661.2000"},{"key":"2025112801450436000_2025.11.24.690211v1.77","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2020.1802866"},{"key":"2025112801450436000_2025.11.24.690211v1.78","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1038\/s41467-021-26392-8","article-title":"Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates","volume":"12","year":"2021","journal-title":"Nat. Commun"},{"key":"2025112801450436000_2025.11.24.690211v1.79","doi-asserted-by":"publisher","DOI":"10.1126\/science.ads0018"},{"key":"2025112801450436000_2025.11.24.690211v1.80","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.03349"},{"key":"2025112801450436000_2025.11.24.690211v1.81","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01688-w"},{"key":"2025112801450436000_2025.11.24.690211v1.82","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-020-0368-1"},{"key":"2025112801450436000_2025.11.24.690211v1.83","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23029-8"},{"key":"2025112801450436000_2025.11.24.690211v1.84","doi-asserted-by":"crossref","first-page":"e0316121","DOI":"10.1128\/mbio.03161-21","article-title":"A Goldilocks principle for the gut microbiome: Taxonomic resolution matters for microbiome-based classification of colorectal cancer","volume":"13","year":"2022","journal-title":"MBio"},{"key":"2025112801450436000_2025.11.24.690211v1.85","doi-asserted-by":"crossref","first-page":"10189","DOI":"10.1038\/s41598-019-46249-x","article-title":"Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data","volume":"9","year":"2019","journal-title":"Sci. Rep"},{"key":"2025112801450436000_2025.11.24.690211v1.86","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-32353-6"},{"key":"2025112801450436000_2025.11.24.690211v1.87","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1707.05005"},{"key":"2025112801450436000_2025.11.24.690211v1.88","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt502"},{"key":"2025112801450436000_2025.11.24.690211v1.89","doi-asserted-by":"crossref","unstructured":"Mallawaarachchi, V. , and Lin, Y . (2022). MetaCoAG: Binning metagenomic contigs via composition, coverage and assembly graphs. In Lecture Notes in Computer Science Lecture notes in computer science. (Springer International Publishing), pp. 70\u201385.","DOI":"10.1007\/978-3-031-04749-7_5"},{"key":"2025112801450436000_2025.11.24.690211v1.90","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts174"},{"key":"2025112801450436000_2025.11.24.690211v1.91","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks678"},{"key":"2025112801450436000_2025.11.24.690211v1.92","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw279"},{"key":"2025112801450436000_2025.11.24.690211v1.93","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"2025112801450436000_2025.11.24.690211v1.94","doi-asserted-by":"crossref","unstructured":"Edmonds, J. , and Johnson, E.L . (2003). Matching: A well-solved class of integer linear programs. In Combinatorial Optimization \u2014 Eureka, You Shrink! Lecture notes in computer science. (Springer Berlin Heidelberg), pp. 27\u201330.","DOI":"10.1007\/3-540-36478-1_3"},{"key":"2025112801450436000_2025.11.24.690211v1.95","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"2025112801450436000_2025.11.24.690211v1.96","unstructured":"Li, H. (2014). A proposal of the Grapical Fragment Assembly format. https:\/\/lh3.github.io\/2014\/07\/19\/a-proposal-of-the-grapical-fragment-assembly-format."},{"key":"2025112801450436000_2025.11.24.690211v1.97","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"2025112801450436000_2025.11.24.690211v1.98","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7359"},{"key":"2025112801450436000_2025.11.24.690211v1.99","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac672"},{"key":"2025112801450436000_2025.11.24.690211v1.100","doi-asserted-by":"publisher","DOI":"10.1609\/icwsm.v3i1.13937"},{"key":"2025112801450436000_2025.11.24.690211v1.101","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0098679"},{"key":"2025112801450436000_2025.11.24.690211v1.102","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"2025112801450436000_2025.11.24.690211v1.103","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr708"},{"key":"2025112801450436000_2025.11.24.690211v1.104","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-00971-x"},{"key":"2025112801450436000_2025.11.24.690211v1.105","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"2025112801450436000_2025.11.24.690211v1.106","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07641-9"},{"key":"2025112801450436000_2025.11.24.690211v1.107","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"2025112801450436000_2025.11.24.690211v1.108","unstructured":"Ke, G. , Meng, Q. , Finley, T. , Wang, T. , Chen, W. , Ma, W. , Ye, Q. , and Liu, T.-Y . (2017). LightGBM: a highly efficient gradient boosting decision tree. In Proceedings of the 31st International Conference on Neural Information Processing Systems NIPS\u201917. (Curran Associates Inc.), pp. 3149\u20133157."},{"key":"2025112801450436000_2025.11.24.690211v1.109","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression shrinkage and selection via the lasso","volume":"58","year":"1996","journal-title":"Journal of the royal statistical society series b-methodological"},{"key":"2025112801450436000_2025.11.24.690211v1.110","unstructured":"Lundberg, S. , and Lee, S.-I. (2017). A unified approach to interpreting model predictions. arXiv [cs.AI]."},{"key":"2025112801450436000_2025.11.24.690211v1.111","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"2025112801450436000_2025.11.24.690211v1.112","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv383"},{"key":"2025112801450436000_2025.11.24.690211v1.113","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00573-18"},{"key":"2025112801450436000_2025.11.24.690211v1.114","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkac114"},{"key":"2025112801450436000_2025.11.24.690211v1.115","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000132"},{"key":"2025112801450436000_2025.11.24.690211v1.116","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0072-8"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.11.24.690211","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T10:05:38Z","timestamp":1768471538000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.11.24.690211"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,26]]},"references-count":116,"URL":"https:\/\/doi.org\/10.1101\/2025.11.24.690211","relation":{},"subject":[],"published":{"date-parts":[[2025,11,26]]},"subtype":"preprint"}}