{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T14:58:52Z","timestamp":1785855532218,"version":"3.56.0"},"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T00:00:00Z","timestamp":1714089600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI148049"],"award-info":[{"award-number":["R01AI148049"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI148049"],"award-info":[{"award-number":["R01AI148049"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI148049"],"award-info":[{"award-number":["R01AI148049"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DP2DA056130"],"award-info":[{"award-number":["DP2DA056130"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R35HG011944"],"award-info":[{"award-number":["R35HG011944"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","award":["MD-GEM training grant"],"award-info":[{"award-number":["MD-GEM training grant"]}],"id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped\/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference\n                    <jats:italic>a priori<\/jats:italic>\n                    remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative \u2018genome graph\u2019 can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual\u2019s infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0301069","type":"journal-article","created":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T13:27:20Z","timestamp":1714138040000},"page":"e0301069","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5629-2012","authenticated-orcid":true,"given":"Dylan","family":"Duchen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven J.","family":"Clipman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Candelaria","family":"Vergara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chloe L.","family":"Thio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David L.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priya","family":"Duggal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Genevieve L.","family":"Wojcik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,4,26]]},"reference":[{"key":"pone.0301069.ref001","author":"WHO","year":"2015","journal-title":"Preventing Perinatal Hepatitis B Virus Transmission: A Guide for Introducing and Strengthening Hepatitis B Birth Dose Vaccination"},{"key":"pone.0301069.ref002","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1016\/S2468-1253(19)30190-6","article-title":"Targets and future direct-acting antiviral approaches to achieve hepatitis B virus cure","volume":"4","author":"T Asselah","year":"2019","journal-title":"The Lancet Gastroenterology & Hepatology"},{"key":"pone.0301069.ref003","first-page":"1","article-title":"Host Genetic Determinants of Hepatitis B Virus Infection","volume":"10","author":"Z Zhang","year":"2019","journal-title":"Frontiers in Genetics"},{"key":"pone.0301069.ref004","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1016\/S0140-6736(14)60220-8","article-title":"Hepatitis B virus infection","volume":"384","author":"C Tr\u00e9po","year":"2014","journal-title":"The Lancet"},{"key":"pone.0301069.ref005","doi-asserted-by":"crossref","first-page":"10529","DOI":"10.1038\/s41598-019-46609-7","article-title":"Large-scale viral genome analysis identifies novel clinical associations between hepatitis B virus and chronically infected patients","volume":"9","author":"O Podlaha","year":"2019","journal-title":"Scientific Reports"},{"key":"pone.0301069.ref006","article-title":"Chronic active hepatitis with hepatitis B virus DNA and antibody against e antigen in the serum. Disturbed synthesis and secretion of e antigen from hepatocytes due to a point mutation in the precore region","author":"Y Akahane","year":"1990","journal-title":"Gastroenterology"},{"key":"pone.0301069.ref007","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1086\/592571","article-title":"Are hepatitis B e antigen (HBeAg)-positive chronic hepatitis B and HBeAg-negative chronic hepatitis B distinct diseases? Clinical infectious diseases: an official publication of the","volume":"47","author":"MH Nguyen","year":"2008","journal-title":"Infectious Diseases Society of America"},{"key":"pone.0301069.ref008","doi-asserted-by":"crossref","first-page":"5761","DOI":"10.3748\/wjg.15.5761","article-title":"Clinical relevance and public health significance of hepatitis B virus genomic variations","volume":"15","author":"G-W Cao","year":"2009","journal-title":"World journal of gastroenterology"},{"key":"pone.0301069.ref009","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1053\/j.gastro.2018.07.058","article-title":"Insights From Deep Sequencing of the HBV Genome\u2014Unique, Tiny, and Misunderstood","volume":"156","author":"AL McNaughton","year":"2018","journal-title":"Gastroenterology"},{"key":"pone.0301069.ref010","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1002\/hep.21188","article-title":"Impact of the hepatitis B virus genotype and genotype mixtures on the course of liver disease in Vietnam","volume":"43","author":"NL Toan","year":"2006","journal-title":"Hepatology"},{"key":"pone.0301069.ref011","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1002\/jmv.23965","article-title":"Molecular epidemiological study of hepatitis B virus genotypes in Southwest, China","volume":"86","author":"L Shen","year":"2014","journal-title":"Journal of Medical Virology"},{"key":"pone.0301069.ref012","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.meegid.2017.10.023","article-title":"Novel HBV recombinants between genotypes B and C in 3\u2032-terminal reverse transcriptase (RT) sequences are associated with enhanced viral DNA load, higher RT point mutation rates and place of birth among Chinese patients","volume":"57","author":"B Liu","year":"2018","journal-title":"Infection, Genetics and Evolution"},{"key":"pone.0301069.ref013","doi-asserted-by":"crossref","first-page":"5657","DOI":"10.1128\/JVI.02556-07","article-title":"New Complex Recombinant Genotype of Hepatitis B Virus Identified in Vietnam","volume":"82","author":"TTT Huy","year":"2008","journal-title":"Journal of Virology"},{"key":"pone.0301069.ref014","doi-asserted-by":"crossref","first-page":"10538","DOI":"10.1128\/JVI.00462-09","article-title":"A Genetic Variant of Hepatitis B Virus Divergent from Known Human and Ape Genotypes Isolated from a Japanese Patient and Provisionally Assigned to New Genotype J","volume":"83","author":"K Tatematsu","year":"2009","journal-title":"Journal of Virology"},{"key":"pone.0301069.ref015","doi-asserted-by":"crossref","first-page":"e941","DOI":"10.1016\/j.ijid.2010.03.020","article-title":"Hepatitis B virus genotyping: Current methods and clinical implications","volume":"14","author":"BSS Guirgis","year":"2010","journal-title":"International Journal of Infectious Diseases"},{"key":"pone.0301069.ref016","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.meegid.2013.03.021","article-title":"Hepatitis B virus subgenotyping: History, effects of recombination, misclassifications, and corrections","volume":"16","author":"W Shi","year":"2013","journal-title":"Infection, Genetics and Evolution"},{"key":"pone.0301069.ref017","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.coviro.2017.03.013","article-title":"Virus population dynamics during infection","volume":"23","author":"EZ Poirier","year":"2017","journal-title":"Current Opinion in Virology"},{"key":"pone.0301069.ref018","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/s41598-017-00694-8","article-title":"Evolution of full-length genomes of HBV quasispecies in sera of patients with a coexistence of HBsAg and anti-HBs antibodies","volume":"7","author":"T-C Zhou","year":"2017","journal-title":"Scientific Reports"},{"key":"pone.0301069.ref019","doi-asserted-by":"crossref","first-page":"2203","DOI":"10.1128\/JCM.00068-15","article-title":"Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection","volume":"53","author":"Z-T Yang","year":"2015","journal-title":"Journal of Clinical Microbiology"},{"key":"pone.0301069.ref020","doi-asserted-by":"crossref","first-page":"e1008271","DOI":"10.1371\/journal.pgen.1008271","article-title":"Viral quasispecies","volume":"15","author":"E Domingo","year":"2019","journal-title":"PLoS Genet"},{"key":"pone.0301069.ref021","doi-asserted-by":"crossref","first-page":"8656","DOI":"10.1128\/JVI.01123-14","article-title":"Coexistence of Hepatitis B Virus Quasispecies Enhances Viral Replication and the Ability To Induce Host Antibody and Cellular Immune Responses","volume":"88","author":"L Cao","year":"2014","journal-title":"Journal of Virology"},{"key":"pone.0301069.ref022","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1007\/s00535-017-1334-1","article-title":"Deep sequencing analysis of quasispecies in the HBV pre-S region and its association with hepatocellular carcinoma","volume":"52","author":"AY Zhang","year":"2017","journal-title":"Journal of Gastroenterology"},{"key":"pone.0301069.ref023","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1136\/gutjnl-2012-302408","article-title":"Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion","volume":"62","author":"Y Cheng","year":"2013","journal-title":"Gut"},{"key":"pone.0301069.ref024","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.cmi.2015.10.007","article-title":"Increased intrahepatic quasispecies heterogeneity correlates with off-treatment sustained response to nucleos(t)ide analogues in e antigen-positive chronic hepatitis B patients","volume":"22","author":"L Chen","year":"2016","journal-title":"Clinical Microbiology and Infection"},{"key":"pone.0301069.ref025","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1136\/gut.2010.226225","article-title":"Evolutionary patterns of hepatitis B virus quasispecies under different selective pressures: correlation with antiviral efficacy","volume":"60","author":"F Liu","year":"2011","journal-title":"Gut"},{"key":"pone.0301069.ref026","doi-asserted-by":"crossref","first-page":"eabg0821","DOI":"10.1126\/science.abg0821","article-title":"SARS-CoV-2 within-host diversity and transmission","volume":"372","author":"KA Lythgoe","year":"2021","journal-title":"Science"},{"key":"pone.0301069.ref027","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1046\/j.1365-2893.1997.00066.x","article-title":"Hepatitis B virus genomic heterogeneity: Variation between quasispecies may confound molecular epidemiological analyses of transmission incidents","volume":"4","author":"SL Ngui","year":"1997","journal-title":"Journal of Viral Hepatitis"},{"key":"pone.0301069.ref028","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.jinf.2017.04.012","article-title":"Quasispecies characteristics in mother-to-child transmission of hepatitis B virus by next-generation sequencing","volume":"75","author":"G Yang","year":"2017","journal-title":"J Infect"},{"key":"pone.0301069.ref029","doi-asserted-by":"crossref","first-page":"5077","DOI":"10.1038\/s41598-022-09035-w","article-title":"The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction","volume":"12","author":"N Moshiri","year":"2022","journal-title":"Scientific Reports"},{"key":"pone.0301069.ref030","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1038\/nprot.2017.066","article-title":"Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples","volume":"12","author":"J Quick","year":"2017","journal-title":"Nature Protocols"},{"key":"pone.0301069.ref031","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1186\/s12879-017-2697-x","article-title":"Molecular characterization of hepatitis B virus in Vietnam","volume":"17","author":"TTT Bui","year":"2017","journal-title":"BMC Infectious Diseases"},{"key":"pone.0301069.ref032","doi-asserted-by":"crossref","first-page":"7081","DOI":"10.1038\/s41598-019-43524-9","article-title":"Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)","volume":"9","author":"AL McNaughton","year":"2019","journal-title":"Scientific Reports"},{"key":"pone.0301069.ref033","doi-asserted-by":"crossref","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":"E Garrison","year":"2018","journal-title":"Nature Biotechnology"},{"key":"pone.0301069.ref034","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/s12072-015-9645-x","article-title":"Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus","volume":"10","author":"W-C Liu","year":"2016","journal-title":"Hepatology International"},{"key":"pone.0301069.ref035","doi-asserted-by":"crossref","first-page":"e1008678","DOI":"10.1371\/journal.pcbi.1008678","article-title":"One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads","volume":"17","author":"C Valiente-Mullor","year":"2021","journal-title":"PLOS Computational Biology"},{"key":"pone.0301069.ref036","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1186\/s13059-021-02473-1","article-title":"Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs","volume":"22","author":"RM Colquhoun","year":"2021","journal-title":"Genome Biology"},{"key":"pone.0301069.ref037","article-title":"Reference genome choice and filtering thresholds jointly influence phylogenomic analyses","author":"JA Rick","year":"2022","journal-title":"bioRxiv"},{"key":"pone.0301069.ref038","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1099\/jgv.0.001387","article-title":"Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences","volume":"101","author":"AL McNaughton","year":"2020","journal-title":"Journal of General Virology"},{"key":"pone.0301069.ref039","doi-asserted-by":"crossref","DOI":"10.1146\/annurev-genom-120219-080406","article-title":"Pangenome Graphs","volume":"21","author":"JM Eizenga","year":"2020","journal-title":"Annual Review of Genomics and Human Genetics"},{"key":"pone.0301069.ref040","doi-asserted-by":"crossref","first-page":"5139","DOI":"10.1093\/bioinformatics\/btaa640","article-title":"Efficient dynamic variation graphs","volume":"36","author":"JM Eizenga","year":"2021","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref041","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/ng.3257","article-title":"Improved genome inference in the MHC using a population reference graph","volume":"47","author":"A Dilthey","year":"2015","journal-title":"Nature Genetics"},{"key":"pone.0301069.ref042","doi-asserted-by":"crossref","first-page":"495","DOI":"10.3390\/genes9100495","article-title":"The Global Hepatitis B Virus Genotype Distribution Approximated from Available Genotyping Data","volume":"9","author":"S Velkov","year":"2018","journal-title":"Genes"},{"key":"pone.0301069.ref043","doi-asserted-by":"crossref","first-page":"5985","DOI":"10.1128\/JVI.76.12.5985-5992.2002","article-title":"Hepatitis B Virus of Genotype B with or without Recombination with Genotype C over the Precore Region plus the Core Gene","volume":"76","author":"F Sugauchi","year":"2002","journal-title":"Journal of Virology"},{"key":"pone.0301069.ref044","doi-asserted-by":"crossref","first-page":"217","DOI":"10.3390\/v14020217","article-title":"ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection","volume":"14","author":"FZ Dezordi","year":"2022","journal-title":"Viruses"},{"key":"pone.0301069.ref045","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1038\/s41467-022-28852-1","article-title":"Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data","volume":"13","author":"Y Liu","year":"2022","journal-title":"Nature Communications"},{"key":"pone.0301069.ref046","first-page":"1","article-title":"Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history","volume":"18","author":"YO Zhu","year":"2017","journal-title":"BMC Genomics"},{"key":"pone.0301069.ref047","doi-asserted-by":"crossref","first-page":"7171","DOI":"10.1128\/JVI.00243-16","article-title":"Single-Molecule Sequencing Reveals Complex Genome Variation of Hepatitis B Virus during 15 Years of Chronic Infection following Liver Transplantation","volume":"90","author":"BD Betz-Stablein","year":"2016","journal-title":"Journal of Virology"},{"key":"pone.0301069.ref048","doi-asserted-by":"crossref","first-page":"146387","DOI":"10.1016\/j.gene.2022.146387","article-title":"Role of genomics in combating COVID-19 pandemic","volume":"823","author":"KA Saravanan","year":"2022","journal-title":"Gene"},{"key":"pone.0301069.ref049","first-page":"2","article-title":"GISAID: Global initiative on sharing all influenza data\u2013from vision to reality","volume":"22","author":"Y Shu","year":"2017","journal-title":"Eurosurveillance"},{"key":"pone.0301069.ref050","first-page":"4121","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"J Hadfield","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pone.0301069.ref051","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1056\/NEJMsr1813907","article-title":"Pathogen Genomics in Public Health","volume":"381","author":"GL Armstrong","year":"2019","journal-title":"New England Journal of Medicine"},{"key":"pone.0301069.ref052","first-page":"1","article-title":"A variant selection framework for genome graphs","author":"C Jain","year":"2021","journal-title":"bioRxiv"},{"key":"pone.0301069.ref053","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s13059-018-1595-x","article-title":"FORGe: prioritizing variants for graph genomes","volume":"19","author":"J Pritt","year":"2018","journal-title":"Genome Biology"},{"key":"pone.0301069.ref054","doi-asserted-by":"crossref","DOI":"10.1515\/jib-2021-0032","article-title":"Fast alignment of reads to a variation graph with application to SNP detection","volume":"18","author":"M Monsu","year":"2021","journal-title":"Journal of Integrative Bioinformatics"},{"key":"pone.0301069.ref055","article-title":"Computational graph pangenomics: a tutorial on data structures and their applications","volume":"6","author":"JA Baaijens","year":"2022","journal-title":"Natural Computing"},{"key":"pone.0301069.ref056","article-title":"Improved sequence mapping using a complete reference genome and lift-over","author":"N Chen","year":"2022","journal-title":"bioRxiv"},{"key":"pone.0301069.ref057","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-020-02229-3","article-title":"Reference flow: reducing reference bias using multiple population genomes","volume":"22","author":"N-C Chen","year":"2021","journal-title":"Genome Biology"},{"key":"pone.0301069.ref058","first-page":"68","article-title":"GEDEVO: An evolutionary graph edit distance algorithm for biological network alignment","volume":"34","author":"R Ibragimov","year":"2013","journal-title":"OpenAccess Series in Informatics"},{"key":"pone.0301069.ref059","article-title":"The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance","author":"Y Qiu","year":"2022","journal-title":"bioRxiv"},{"key":"pone.0301069.ref060","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1038\/s41586-023-05896-x","article-title":"A draft human pangenome reference","volume":"617","author":"W-W Liao","year":"2023","journal-title":"Nature"},{"key":"pone.0301069.ref061","doi-asserted-by":"crossref","first-page":"eaau6905","DOI":"10.1126\/sciimmunol.aau6905","article-title":"Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection","volume":"4","author":"Y Cheng","year":"2019","journal-title":"Science Immunology"},{"key":"pone.0301069.ref062","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M. Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"pone.0301069.ref063","article-title":"FastQC","author":"S. Andrews","year":"2010","journal-title":"Babraham Bioinformatics"},{"key":"pone.0301069.ref064","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/bty630","article-title":"Simulating Illumina metagenomic data with InSilicoSeq","volume":"35","author":"H Gourl\u00e9","year":"2019","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref065","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/btaa777","article-title":"Fast gap-affine pairwise alignment using the wavefront algorithm","volume":"37","author":"S Marco-Sola","year":"2021","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref066","doi-asserted-by":"crossref","first-page":"btac743","DOI":"10.1093\/bioinformatics\/btac743","article-title":"Unbiased pangenome graphs","volume":"39","author":"E Garrison","year":"2023","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref067","article-title":"Building pangenome graphs","author":"E Garrison","year":"2023","journal-title":"bioRxiv"},{"key":"pone.0301069.ref068","doi-asserted-by":"crossref","DOI":"10.1126\/science.abg8871","article-title":"Pangenomics enables genotyping of known structural variants in 5202 diverse genomes","volume":"374","author":"J Sir\u00e9n","year":"2021","journal-title":"Science"},{"key":"pone.0301069.ref069","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1093\/bioinformatics\/btz575","article-title":"Haplotype-aware graph indexes","volume":"36","author":"J Sir\u00e9n","year":"2018","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref070","doi-asserted-by":"crossref","first-page":"3941","DOI":"10.21105\/joss.03941","article-title":"Rasusa: Randomly subsample sequencing reads to a specified coverage","volume":"7","author":"M. Hall","year":"2022","journal-title":"Journal of Open Source Software"},{"key":"pone.0301069.ref071","first-page":"2078","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pone.0301069.ref072","first-page":"419","article-title":"pegas: an R package for population genetics with an integrated-modular approach","volume":"26","author":"E. Paradis","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pone.0301069.ref073","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"H. Li","year":"2013","journal-title":"arXiv"},{"key":"pone.0301069.ref074","first-page":"292","article-title":"Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data","volume":"32","author":"K Okonechnikov","year":"2016","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pone.0301069.ref075","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: interactive visualization of de novo genome assemblies: Fig 1","volume":"31","author":"RR Wick","year":"2015","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref076","doi-asserted-by":"crossref","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":"G Holley","year":"2020","journal-title":"Genome Biology"},{"key":"pone.0301069.ref077","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"ND Grubaugh","year":"2019","journal-title":"Genome Biology"},{"key":"pone.0301069.ref078","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"P Danecek","year":"2021","journal-title":"GigaScience"},{"key":"pone.0301069.ref079","author":"B. Bushnell","year":"2014","journal-title":"BBMap: A Fast, Accurate, Splice-Aware Aligner"},{"key":"pone.0301069.ref080","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","article-title":"PEAR: a fast and accurate Illumina Paired-End reAd mergeR","volume":"30","author":"J Zhang","year":"2014","journal-title":"Bioinformatics"},{"key":"pone.0301069.ref081","doi-asserted-by":"crossref","first-page":"11189","DOI":"10.1093\/nar\/gks918","article-title":"LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets","volume":"40","author":"A Wilm","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"pone.0301069.ref082","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"BD Ondov","year":"2016","journal-title":"Genome Biology"},{"key":"pone.0301069.ref083","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0206409","article-title":"An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes","volume":"13","author":"S Solis-Reyes","year":"2018","journal-title":"PLoS ONE"},{"key":"pone.0301069.ref084","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s40168-017-0283-5","article-title":"VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data","volume":"5","author":"J Ren","year":"2017","journal-title":"Microbiome"},{"key":"pone.0301069.ref085","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1101\/gr.215038.116","article-title":"De novo assembly of viral quasispecies using overlap graphs","volume":"27","author":"JA Baaijens","year":"2017","journal-title":"Genome Research"},{"key":"pone.0301069.ref086","first-page":"645721","article-title":"Strain-aware assembly of genomes from mixed samples using flow variation graphs","author":"JA Baaijens","year":"2020","journal-title":"bioRxiv"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0301069","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,26]],"date-time":"2024-04-26T13:28:05Z","timestamp":1714138085000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0301069"}},"subtitle":[],"editor":[{"given":"Isabelle","family":"Chemin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,4,26]]},"references-count":86,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2024,4,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0301069","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.01.11.523611","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,26]]}}}