{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T03:22:32Z","timestamp":1774408952542,"version":"3.50.1"},"reference-count":110,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,18]],"date-time":"2024-11-18T00:00:00Z","timestamp":1731888000000},"content-version":"vor","delay-in-days":56,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Pangenomes have emerged in response to limitations associated with traditional linear reference genomes. In contrast to a traditional reference that is (usually) assembled from a single individual, pangenomes aim to represent all of the genomic variation found in a group of organisms. The term \u2018pangenome\u2019 is currently used to describe multiple different types of genomic information, and limited language is available to differentiate between them. This is frustrating for researchers working in the field and confusing for researchers new to the field. Here, we provide an introduction to pangenomics relevant to both prokaryotic and eukaryotic organisms and propose a formalization of the language used to describe pangenomes (see the Glossary) to improve the specificity of discussion in the field.<\/jats:p>","DOI":"10.1093\/bib\/bbae588","type":"journal-article","created":{"date-parts":[[2024,11,18]],"date-time":"2024-11-18T05:24:43Z","timestamp":1731907483000},"source":"Crossref","is-referenced-by-count":32,"title":["A gentle introduction to pangenomics"],"prefix":"10.1093","volume":"25","author":[{"given":"Chelsea A","family":"Matthews","sequence":"first","affiliation":[{"name":"School of Agriculture , Food and Wine, Waite Campus, , Urrbrae, South Australia 5064 ,","place":["Australia"]},{"name":"University of Adelaide , Food and Wine, Waite Campus, , Urrbrae, South Australia 5064 ,","place":["Australia"]}]},{"given":"Nathan S","family":"Watson-Haigh","sequence":"additional","affiliation":[{"name":"Australian Genome Research Facility, Victorian Comprehensive Cancer Centre , Melbourne, Victoria 3000 ,","place":["Australia"]},{"name":"South Australian Genomics Centre, SAHMRI , North Terrace, Adelaide, South Australia 5000 ,","place":["Australia"]},{"name":"Alkahest Inc. , San Carlos, CA 94070 ,","place":["United States"]}]},{"given":"Rachel A","family":"Burton","sequence":"additional","affiliation":[{"name":"School of Agriculture , Food and Wine, Waite Campus, , Urrbrae, South Australia 5064 ,","place":["Australia"]},{"name":"University of Adelaide , Food and Wine, Waite Campus, , Urrbrae, South Australia 5064 ,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2913-0920","authenticated-orcid":false,"given":"Anna E","family":"Sheppard","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, University of Adelaide , Adelaide, South Australia 5005 ,","place":["Australia"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,17]]},"reference":[{"key":"2024111805243204700_ref1","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/bfgp\/elu016","article-title":"Structural variations in plant genomes","volume":"13","author":"Saxena","year":"2014","journal-title":"Brief Funct Genomics"},{"key":"2024111805243204700_ref2","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1186\/s13059-019-1774-4","article-title":"Is it time to change the reference genome?","volume":"20","author":"Ballouz","year":"2019","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref3","doi-asserted-by":"publisher","first-page":"180069","DOI":"10.3835\/plantgenome2018.09.0069","article-title":"Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel","volume":"12","author":"Gage","year":"2019","journal-title":"Plant Genome"},{"key":"2024111805243204700_ref4","doi-asserted-by":"publisher","first-page":"i361","DOI":"10.1093\/bioinformatics\/btt215","article-title":"Short read alignment with populations of genomes","volume":"29","author":"Huang","year":"2013","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref5","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/s41587-023-01793-w","article-title":"Pangenome graph construction from genome alignments with Minigraph-cactus","volume":"42","author":"Hickey","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2024111805243204700_ref6","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/nbt.4227","article-title":"Variation graph toolkit improves read mapping by representing genetic variation in the reference","volume":"36","author":"Garrison","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2024111805243204700_ref7","doi-asserted-by":"publisher","first-page":"e2101056118","DOI":"10.1073\/pnas.2101056118","article-title":"Novel functional sequences uncovered through a bovine multiassembly graph","volume":"118","author":"Crysnanto","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024111805243204700_ref8","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/bib\/bbw089","article-title":"Computational pan-genomics: status, promises and challenges","volume":"19","author":"Consortium TCP-G","year":"2018","journal-title":"Brief Bioinform"},{"key":"2024111805243204700_ref9","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.tig.2019.11.006","article-title":"Pangenomics comes of age: from bacteria to plant and animal applications","volume":"36","author":"Golicz","year":"2020","journal-title":"Trends Genet"},{"key":"2024111805243204700_ref10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/ncomms13390","article-title":"The pangenome of an agronomically important crop plant Brassica oleracea","volume":"7","author":"Golicz","year":"2016","journal-title":"Nat Commun"},{"key":"2024111805243204700_ref11","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s12864-018-4465-8","article-title":"Towards pan-genome read alignment to improve variation calling","volume":"19","author":"Valenzuela","year":"2018","journal-title":"BMC Genomics"},{"key":"2024111805243204700_ref12","first-page":"1441","article-title":"Cancer genome or the development of molecular portraits of tumors","volume":"184","author":"Sigaux","year":"2000","journal-title":"Bull Acad Natl Med"},{"key":"2024111805243204700_ref13","doi-asserted-by":"publisher","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc Natl Acad Sci"},{"key":"2024111805243204700_ref14","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/s41586-018-0063-9","article-title":"Genomic variation in 3,010 diverse accessions of Asian cultivated rice","volume":"557","author":"Wang","year":"2018","journal-title":"Nature"},{"key":"2024111805243204700_ref15","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1016\/j.tig.2008.12.004","article-title":"Estimating the size of the bacterial pan-genome","volume":"25","author":"Lapierre","year":"2009","journal-title":"Trends Genet"},{"key":"2024111805243204700_ref16","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1007\/978-3-030-38281-0_13","volume-title":"Pangenome Divers. Dyn. Evol","author":"Hu","year":"2020"},{"key":"2024111805243204700_ref17","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1111\/pbi.12499","article-title":"Towards plant pangenomics","volume":"14","author":"Golicz","year":"2016","journal-title":"Plant Biotechnol J"},{"key":"2024111805243204700_ref18","doi-asserted-by":"publisher","first-page":"bbaa198","DOI":"10.1093\/bib\/bbaa198","article-title":"Challenges in gene-oriented approaches for pangenome content discovery","volume":"22","author":"Bonnici","year":"2021","journal-title":"Brief Bioinform"},{"key":"2024111805243204700_ref19","doi-asserted-by":"publisher","first-page":"1177932220938064","DOI":"10.1177\/1177932220938064","article-title":"First steps in the analysis of prokaryotic pan-genomes","volume":"14","author":"Costa","year":"2020","journal-title":"Bioinform Biol Insights"},{"key":"2024111805243204700_ref20","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nbt.2979","article-title":"De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits","volume":"32","author":"Li","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2024111805243204700_ref21","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1038\/s41588-018-0041-z","article-title":"Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice","volume":"50","author":"Zhao","year":"2018","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref22","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1038\/s41586-020-2947-8","article-title":"The barley pan-genome reveals the hidden legacy of mutation breeding","volume":"588","author":"Jayakodi","year":"2020","journal-title":"Nature"},{"key":"2024111805243204700_ref23","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s12864-022-08303-3","article-title":"Panakeia - a universal tool for bacterial pangenome analysis","volume":"23","author":"Beier","year":"2022","journal-title":"BMC Genomics"},{"key":"2024111805243204700_ref24","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"Tonkin-Hill","year":"2020","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref25","doi-asserted-by":"publisher","first-page":"e1007732","DOI":"10.1371\/journal.pcbi.1007732","article-title":"PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph","volume":"16","author":"Gautreau","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2024111805243204700_ref26","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1186\/s12859-022-04898-2","article-title":"A graph-based approach for the visualisation and analysis of bacterial pangenomes","volume":"23","author":"Harling-Lee","year":"2022","journal-title":"BMC Bioinformatics"},{"key":"2024111805243204700_ref27","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/s10142-014-0412-1","article-title":"Gene loss in the fungal canola pathogen Leptosphaeria maculans","volume":"15","author":"Golicz","year":"2015","journal-title":"Funct Integr Genomics"},{"key":"2024111805243204700_ref28","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/0888-7543(88)90007-9","article-title":"Genomic mapping by fingerprinting random clones: a mathematical analysis","volume":"2","author":"Lander","year":"1988","journal-title":"Genomics"},{"key":"2024111805243204700_ref29","doi-asserted-by":"publisher","first-page":"5066","DOI":"10.1093\/molbev\/msab231","article-title":"The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size","volume":"38","author":"Wang","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2024111805243204700_ref30","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1038\/s41588-019-0410-2","article-title":"The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor","volume":"51","author":"Gao","year":"2019","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref31","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20100","article-title":"The pangenome of banana highlights differences between genera and genomes","volume":"15","author":"Rijzaani","year":"2022","journal-title":"Plant Genome"},{"key":"2024111805243204700_ref32","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1038\/s41564-021-00993-x","article-title":"Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection","volume":"6","author":"Barber","year":"2021","journal-title":"Nat Microbiol"},{"key":"2024111805243204700_ref33","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s12915-022-01347-7","article-title":"To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131","volume":"20","author":"Tantoso","year":"2022","journal-title":"BMC Biol"},{"key":"2024111805243204700_ref34","doi-asserted-by":"publisher","first-page":"21205","DOI":"10.1038\/s41598-020-77723-6","article-title":"Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order","volume":"10","author":"Gaba","year":"2020","journal-title":"Sci Rep"},{"key":"2024111805243204700_ref35","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1038\/s41467-017-02292-8","article-title":"Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure","volume":"8","author":"Gordon","year":"2017","journal-title":"Nat Commun"},{"key":"2024111805243204700_ref36","doi-asserted-by":"publisher","first-page":"bbac413","DOI":"10.1093\/bib\/bbac413","article-title":"Critical assessment of pan-genomic analysis of metagenome-assembled genomes","volume":"23","author":"Li","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024111805243204700_ref37","doi-asserted-by":"publisher","first-page":"104552","DOI":"10.1016\/j.jbi.2023.104552","article-title":"PanDelos-frags: a methodology for discovering pangenomic content of incomplete microbial assemblies","volume":"148","author":"Bonnici","year":"2023","journal-title":"J Biomed Inform"},{"key":"2024111805243204700_ref38","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1186\/s12864-016-3382-y","article-title":"The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights","volume":"18","author":"Bosi","year":"2017","journal-title":"BMC Genomics"},{"key":"2024111805243204700_ref39","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.copbio.2019.12.001","article-title":"Current status of pan-genome analysis for pathogenic bacteria","volume":"63","author":"Kim","year":"2020","journal-title":"Curr Opin Biotechnol"},{"key":"2024111805243204700_ref40","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1126\/science.1109869","article-title":"Identification of a universal group B streptococcus vaccine by multiple genome screen","volume":"309","author":"Maione","year":"2005","journal-title":"Science"},{"key":"2024111805243204700_ref41","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1126\/science.1111563","article-title":"Genome analysis reveals pili in group B streptococcus","volume":"309","author":"Lauer","year":"2005","journal-title":"Science"},{"key":"2024111805243204700_ref42","doi-asserted-by":"publisher","first-page":"4306","DOI":"10.1038\/s41467-018-06634-y","article-title":"Machine learning and structural analysis of mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance","volume":"9","author":"Kavvas","year":"2018","journal-title":"Nat Commun"},{"key":"2024111805243204700_ref43","doi-asserted-by":"publisher","first-page":"3473","DOI":"10.1073\/pnas.0800151105","article-title":"Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis","volume":"105","author":"Schoen","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024111805243204700_ref44","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/gbe\/evy259","article-title":"The Pseudomonas aeruginosa pan-genome provides new insights on its population structure, horizontal gene transfer, and pathogenicity","volume":"11","author":"Freschi","year":"2019","journal-title":"Genome Biol Evol"},{"key":"2024111805243204700_ref45","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.gene.2017.04.019","article-title":"Pan-genome analysis of clostridium botulinum reveals unique targets for drug development","volume":"623","author":"Bhardwaj","year":"2017","journal-title":"Gene"},{"key":"2024111805243204700_ref46","doi-asserted-by":"publisher","first-page":"819","DOI":"10.3390\/antibiotics9110819","article-title":"Pangenome analysis of mycobacterium tuberculosis reveals Core-drug targets and screening of promising Lead compounds for drug discovery","volume":"9","author":"Dar","year":"2020","journal-title":"Antibiotics"},{"key":"2024111805243204700_ref47","doi-asserted-by":"publisher","first-page":"914","DOI":"10.1038\/s41477-020-0733-0","article-title":"Plant pan-genomes are the new reference","volume":"6","author":"Bayer","year":"2020","journal-title":"Nat Plants"},{"key":"2024111805243204700_ref48","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.tplants.2019.10.012","article-title":"Super-Pangenome by integrating the wild side of a species for accelerated crop improvement","volume":"25","author":"Khan","year":"2020","journal-title":"Trends Plant Sci"},{"key":"2024111805243204700_ref49","doi-asserted-by":"publisher","DOI":"10.1002\/9781119312994.apr0664","article-title":"Plant Pangenome: impacts on phenotypes and evolution","volume":"2","author":"Tranchant-Dubreuil","year":"2019","journal-title":"Annu Plant Rev"},{"key":"2024111805243204700_ref50","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.pbi.2019.12.005","article-title":"Plant pangenomics: approaches, applications and advancements","volume":"54","author":"Danilevicz","year":"2020","journal-title":"Curr Opin Plant Biol"},{"key":"2024111805243204700_ref51","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1186\/s13059-015-0757-3","article-title":"Exploring the rice dispensable genome using a metagenome-like assembly strategy","volume":"16","author":"Yao","year":"2015","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref52","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0301s42","article-title":"An introduction to sequence similarity (\u201chomology\u201d) searching","volume":"42","author":"Pearson","journal-title":"Curr Protoc Bioinform"},{"key":"2024111805243204700_ref53","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref54","doi-asserted-by":"publisher","first-page":"10","DOI":"10.3389\/fgene.2019.01169","article-title":"Towards the complete goat pan-genome by recovering missing genomic segments from the reference genome","volume":"10","author":"Li","year":"2019","journal-title":"Front Genet"},{"key":"2024111805243204700_ref55","doi-asserted-by":"publisher","first-page":"1852","DOI":"10.1111\/pbi.13600","article-title":"The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content","volume":"19","author":"Torkamaneh","year":"2021","journal-title":"Plant Biotechnol J"},{"key":"2024111805243204700_ref56","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1111\/tpj.15313","article-title":"Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding","volume":"107","author":"Barchi","year":"2021","journal-title":"Plant J"},{"key":"2024111805243204700_ref57","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/s13059-021-02351-w","article-title":"Cotton pan-genome retrieves the lost sequences and genes during domestication and selection","volume":"22","author":"Li","year":"2021","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref58","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-021-02556-6","article-title":"Building a Chinese pan-genome of 486 individuals","volume":"4","author":"Li","year":"2021","journal-title":"Commun Biol"},{"key":"2024111805243204700_ref59","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/s13059-015-0587-3","article-title":"Extending reference assembly models","volume":"16","author":"Church","year":"2015","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref60","volume-title":"GRCh38 or hg38 - b37 - hg19. GATK n.d","author":"Human genome reference builds"},{"key":"2024111805243204700_ref61","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1038\/s41586-022-04601-8","article-title":"The Human Pangenome Project: a global resource to map genomic diversity","volume":"604","author":"Wang","year":"2022","journal-title":"Nature"},{"key":"2024111805243204700_ref62","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"2024111805243204700_ref63","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1038\/s41588-018-0273-y","article-title":"Assembly of a pan-genome from deep sequencing of 910 humans of African descent","volume":"51","author":"Sherman","year":"2019","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref64","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1038\/s41587-022-01484-y","volume":"40","author":"One pangenome to bind them all","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2024111805243204700_ref65","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1038\/s41588-018-0316-4","article-title":"Fast and accurate genomic analyses using genome graphs","volume":"51","author":"Rakocevic","year":"2019","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref66","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1007\/978-3-319-43681-4_18","volume-title":"Algorithms Bioinforma","author":"Maciuca","year":"2016"},{"key":"2024111805243204700_ref67","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s13059-020-02168-z","article-title":"The design and construction of reference pangenome graphs with minigraph","volume":"21","author":"Li","year":"2020","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref68","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.12688\/f1000research.15895.2","article-title":"NovoGraph: human genome graph construction from multiple long-read de novo assemblies","volume-title":"F1000Research","author":"Biederstedt","year":"2018"},{"key":"2024111805243204700_ref69","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1186\/s12864-017-4401-3","article-title":"Seq-seq-pan: building a computational pan-genome data structure on whole genome alignment","volume":"19","author":"Jandrasits","year":"2018","journal-title":"BMC Genomics"},{"key":"2024111805243204700_ref70","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s13059-020-1941-7","article-title":"Genotyping structural variants in pangenome graphs using the vg toolkit","volume":"21","author":"Hickey","year":"2020","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref71","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","article-title":"A draft human pangenome reference","volume":"617","author":"Liao","year":"2023","journal-title":"Nature"},{"key":"2024111805243204700_ref72","doi-asserted-by":"publisher","DOI":"10.1101\/175976","article-title":"LOGAN: a framework for LOssless graph-based ANalysis of high throughput sequence data","volume-title":"bioRxiv","author":"Bolger","year":"2017"},{"key":"2024111805243204700_ref73","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.1093\/bioinformatics\/bty157","article-title":"Integrating long-range connectivity information into de Bruijn graphs","volume":"34","author":"Turner","year":"2018","journal-title":"Bioinforma Oxf Engl"},{"key":"2024111805243204700_ref74","doi-asserted-by":"publisher","first-page":"282","DOI":"10.1186\/s12859-021-04149-w","article-title":"A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes","volume":"22","author":"Guo","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2024111805243204700_ref75","doi-asserted-by":"publisher","first-page":"4024","DOI":"10.1093\/bioinformatics\/btw609","article-title":"TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes","volume":"33","author":"Minkin","year":"2017","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref76","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1186\/s13059-020-02135-8","article-title":"Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs","volume":"21","author":"Holley","year":"2020","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref77","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1038\/ng.1028","article-title":"De novo assembly and genotyping of variants using colored de Bruijn graphs","volume":"44","author":"Iqbal","year":"2012","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref78","doi-asserted-by":"publisher","first-page":"abg8871","DOI":"10.1126\/science.abg8871","article-title":"Pangenomics enables genotyping of known structural variants in 5202 diverse genomes","volume":"374","author":"Sir\u00e9n","year":"2021","journal-title":"Science"},{"key":"2024111805243204700_ref79","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1146\/annurev-genom-120219-080406","article-title":"Pangenome graphs","volume":"21","author":"Eizenga","year":"2020","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2024111805243204700_ref80","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/s41588-022-01043-w","article-title":"Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes","volume":"54","author":"Ebler","year":"2022","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref81","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/ng.3257","article-title":"Improved genome inference in the MHC using a population reference graph","volume":"47","author":"Dilthey","year":"2015","journal-title":"Nat Genet"},{"key":"2024111805243204700_ref82","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1186\/s13059-015-0762-6","article-title":"Tools and best practices for data processing in allelic expression analysis","volume":"16","author":"Castel","year":"2015","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref83","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/s12859-017-1678-9","article-title":"Coordinates and intervals in graph-based reference genomes","volume":"18","author":"Rand","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2024111805243204700_ref84","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref85","doi-asserted-by":"publisher","first-page":"2853","DOI":"10.1093\/bioinformatics\/bty1046","article-title":"GfaViz: flexible and interactive visualization of GFA sequence graphs","volume":"35","author":"Gonnella","year":"2019","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref86","doi-asserted-by":"publisher","first-page":"5318","DOI":"10.1093\/bioinformatics\/btz597","article-title":"Sequence tube maps: making graph genomes intuitive to commuters","volume":"35","author":"Beyer","year":"2019","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref87","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.mib.2014.11.016","article-title":"Ten years of pan-genome analyses","volume":"23","author":"Vernikos","year":"2015","journal-title":"Curr Opin Microbiol"},{"key":"2024111805243204700_ref88","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.nmni.2015.06.005","article-title":"The bacterial pangenome as a new tool for analysing pathogenic bacteria","volume":"7","author":"Rouli","year":"2015","journal-title":"New Microbes New Infect"},{"key":"2024111805243204700_ref89","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1101\/gr.180190.114","article-title":"Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains","volume":"25","author":"Salipante","year":"2015","journal-title":"Genome Res"},{"key":"2024111805243204700_ref90","doi-asserted-by":"publisher","first-page":"834","DOI":"10.3389\/fmicb.2019.00834","article-title":"Large-scale genomics reveals the genetic characteristics of seven species and importance of phylogenetic distance for estimating pan-genome size","volume":"10","author":"Park","year":"2019","journal-title":"Front Microbiol"},{"key":"2024111805243204700_ref91","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1186\/s12864-018-4978-1","article-title":"Comparative genomic analysis of staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer","volume":"19","author":"Argemi","year":"2018","journal-title":"BMC Genomics"},{"key":"2024111805243204700_ref92","article-title":"Genetic Perspectives of Germplasm Conservation","volume-title":"Genetic Manipulation: Impact on Man and Society","author":"Frankel","year":"1984"},{"key":"2024111805243204700_ref93","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1007\/s11434-008-0212-x","article-title":"Genetic diversity and construction of core collection in Chinese wheat genetic resources","volume":"53","author":"Hao","year":"2008","journal-title":"Sci Bull"},{"key":"2024111805243204700_ref94","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.cj.2016.10.006","article-title":"Genomics-based plant germplasm research (GPGR)","volume":"5","author":"Jia","year":"2017","journal-title":"Crop J"},{"key":"2024111805243204700_ref95","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1186\/s12859-018-2209-z","article-title":"Core hunter 3: flexible core subset selection","volume":"19","author":"De Beukelaer","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2024111805243204700_ref96","doi-asserted-by":"publisher","first-page":"2155","DOI":"10.1093\/bioinformatics\/btm313","article-title":"PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets","volume":"23","author":"Kim","year":"2007","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref97","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1186\/s13059-018-1595-x","article-title":"FORGe: prioritizing variants for graph genomes","volume":"19","author":"Pritt","year":"2018","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref98","doi-asserted-by":"publisher","first-page":"4384","DOI":"10.1038\/s41467-022-31724-3","article-title":"Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis","volume":"13","author":"Tetikol","year":"2022","journal-title":"Nat Commun"},{"key":"2024111805243204700_ref99","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1186\/s13059-020-02105-0","article-title":"Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery","volume":"21","author":"Crysnanto","year":"2020","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref100","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1186\/s13059-023-03089-3","article-title":"Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses","volume":"24","author":"Manzano-Morales","year":"2023","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref101","doi-asserted-by":"publisher","first-page":"001021","DOI":"10.1099\/mgen.0.001021","article-title":"Challenges in prokaryote pangenomics. Microb","volume":"9","author":"Tonkin-Hill","year":"2023","journal-title":"Genomics"},{"key":"2024111805243204700_ref102","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1093\/bioinformatics\/btx170","article-title":"EUPAN enables pan-genome studies of a large number of eukaryotic genomes","volume":"33","author":"Hu","year":"2017","journal-title":"Bioinformatics"},{"key":"2024111805243204700_ref103","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1186\/s13059-019-1751-y","article-title":"HUPAN: a pan-genome analysis pipeline for human genomes","volume":"20","author":"Duan","year":"2019","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref104","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1111\/1755-0998.13344","article-title":"Panoramic: a package for constructing eukaryotic pan-genomes","volume":"21","author":"Glick","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2024111805243204700_ref105","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1038\/s41477-018-0329-0","article-title":"Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance","volume":"5","author":"H\u00fcbner","year":"2019","journal-title":"Nat Plants"},{"key":"2024111805243204700_ref106","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1111\/tpj.13515","article-title":"The pangenome of hexaploid bread wheat","volume":"90","author":"Montenegro","year":"2017","journal-title":"Plant J"},{"key":"2024111805243204700_ref107","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1186\/s13059-023-03098-2","article-title":"Comparing methods for constructing and representing human pangenome graphs","volume":"24","author":"Andreace","year":"2023","journal-title":"Genome Biol"},{"key":"2024111805243204700_ref108","doi-asserted-by":"publisher","first-page":"001034","DOI":"10.1099\/mgen.0.001034","article-title":"PanGraph: scalable bacterial pan-genome graph construction","volume":"9","author":"Noll","year":"2023","journal-title":"Microb Genomics"},{"key":"2024111805243204700_ref109","doi-asserted-by":"publisher","first-page":"05.535718","DOI":"10.1101\/2023.04.05.535718","volume":"2023","author":"Garrison","year":"2023","journal-title":"Building pangenome graphs"},{"key":"2024111805243204700_ref110","doi-asserted-by":"publisher","first-page":"btac743","DOI":"10.1093\/bioinformatics\/btac743","article-title":"Unbiased pangenome graphs","volume":"39","author":"Garrison","year":"2023","journal-title":"Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae588\/60702740\/bbae588.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/6\/bbae588\/60702740\/bbae588.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,18]],"date-time":"2024-11-18T05:24:49Z","timestamp":1731907489000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae588\/7902219"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,23]]},"references-count":110,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,9,23]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae588","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,11]]},"published":{"date-parts":[[2024,9,23]]},"article-number":"bbae588"}}