{"id":"https://openalex.org/W4392543504","doi":"https://doi.org/10.1109/tcbb.2024.3374595","title":"ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data","display_name":"ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data","publication_year":2024,"publication_date":"2024-03-07","ids":{"openalex":"https://openalex.org/W4392543504","doi":"https://doi.org/10.1109/tcbb.2024.3374595","pmid":"https://pubmed.ncbi.nlm.nih.gov/38451771"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3374595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3374595","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104668217","display_name":"Weiling Li","orcid":"https://orcid.org/0000-0002-3492-3888"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weiling Li","raw_affiliation_strings":["Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA","Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, USA"],"raw_orcid":"https://orcid.org/0000-0002-3492-3888","affiliations":[{"raw_affiliation_string":"Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107809194","display_name":"Raunaq Malhotra","orcid":"https://orcid.org/0000-0002-7253-850X"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raunaq Malhotra","raw_affiliation_strings":["ScienceIO, New York, NY, USA","School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, USA"],"raw_orcid":"https://orcid.org/0000-0002-7253-850X","affiliations":[{"raw_affiliation_string":"ScienceIO, New York, NY, USA","institution_ids":[]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025044285","display_name":"Steven Wu","orcid":"https://orcid.org/0000-0002-7685-8009"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Steven Wu","raw_affiliation_strings":["Department of Agronomy, National Taiwan University, Taipei, Taiwan","BioConsortia, Inc. Davis, USA"],"raw_orcid":"https://orcid.org/0000-0002-7685-8009","affiliations":[{"raw_affiliation_string":"Department of Agronomy, National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"BioConsortia, Inc. Davis, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058764978","display_name":"Manjari Jha","orcid":"https://orcid.org/0000-0002-7817-4233"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manjari Jha","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, PA, USA","School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, USA"],"raw_orcid":"https://orcid.org/0000-0002-7817-4233","affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015045944","display_name":"Allen G. Rodrigo","orcid":"https://orcid.org/0000-0002-8327-7317"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Allen Rodrigo","raw_affiliation_strings":["School of Biological Sciences, University of Auckland, Private Bag, New Zealand","School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-8327-7317","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, University of Auckland, Private Bag, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080238858","display_name":"Mary Poss","orcid":"https://orcid.org/0000-0003-4147-2410"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary Poss","raw_affiliation_strings":["Department of Hematology and Oncology, School of Medicine, University of Virginia, Charlottesville, VA, USA","Department of Biology, Pennsylvania State University, University Park, USA"],"raw_orcid":"https://orcid.org/0000-0003-4147-2410","affiliations":[{"raw_affiliation_string":"Department of Hematology and Oncology, School of Medicine, University of Virginia, Charlottesville, VA, USA","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Biology, Pennsylvania State University, University Park, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023786448","display_name":"Raj Acharya","orcid":"https://orcid.org/0009-0001-7142-5538"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raj Acharya","raw_affiliation_strings":["Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA"],"raw_orcid":"https://orcid.org/0009-0001-7142-5538","affiliations":[{"raw_affiliation_string":"Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":0.4765,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.59318878,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"21","issue":"3","first_page":"492","last_page":"500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11112","display_name":"Viral Infections and Immunology Research","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.4944572448730469},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4941721260547638},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4238974452018738},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3441319465637207},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.11913955211639404}],"concepts":[{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.4944572448730469},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4941721260547638},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4238974452018738},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3441319465637207},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.11913955211639404}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006678","descriptor_name":"HIV","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3374595","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3374595","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38451771","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38451771","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.5799999833106995}],"awards":[{"id":"https://openalex.org/G4938157959","display_name":null,"funder_award_id":"1724008","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G6693054683","display_name":null,"funder_award_id":"1720635","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1975963573","https://openalex.org/W2025161234","https://openalex.org/W2027969303","https://openalex.org/W2033328184","https://openalex.org/W2047516879","https://openalex.org/W2057253402","https://openalex.org/W2063797600","https://openalex.org/W2073918065","https://openalex.org/W2105757606","https://openalex.org/W2107772251","https://openalex.org/W2110233077","https://openalex.org/W2120902911","https://openalex.org/W2121942252","https://openalex.org/W2125266506","https://openalex.org/W2126924325","https://openalex.org/W2128868625","https://openalex.org/W2131271579","https://openalex.org/W2134053782","https://openalex.org/W2153737961","https://openalex.org/W2164971951","https://openalex.org/W2167469524","https://openalex.org/W2282281992","https://openalex.org/W2738888826","https://openalex.org/W2789208418","https://openalex.org/W2804624135","https://openalex.org/W2895878640","https://openalex.org/W2949491511","https://openalex.org/W2996751484","https://openalex.org/W3001897055","https://openalex.org/W3009934907","https://openalex.org/W3011537081","https://openalex.org/W3029338293","https://openalex.org/W3036113864","https://openalex.org/W3039901154","https://openalex.org/W3040594304","https://openalex.org/W3040739570","https://openalex.org/W3044443183","https://openalex.org/W3093842248"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191"],"abstract_inverted_index":{"We":[0,61,107],"present":[1],"ViPRA-Haplo,":[2,130],"a":[3,14,32,37,100,174],"de":[4],"novo":[5],"strain-specific":[6],"assembly":[7],"workflow":[8],"for":[9],"reconstructing":[10],"viral":[11,15,74,105,116,166],"haplotypes":[12],"in":[13,135,200,226],"population":[16,167],"from":[17,36,119,124],"paired-end":[18],"next":[19],"generation":[20],"sequencing":[21,204,228],"(NGS)":[22],"data.":[23,156,229],"The":[24,49,76],"proposed":[25],"Viral":[26],"Path":[27],"Reconstruction":[28],"Algorithm":[29],"(ViPRA)":[30],"generates":[31,99],"subset":[33],"of":[34,41,47,57,71,104,138,164,173,177,214],"paths":[35,50,80],"De":[38],"Bruijn":[39],"graph":[40],"reads":[42],"using":[43,84],"the":[44,58,95,136,142,165,171,215,227],"pairing":[45],"information":[46],"reads.":[48],"generated":[51],"by":[52,82,170],"ViPRA":[53,83],"are":[54,198],"an":[55,68,133],"over-estimation":[56],"true":[59,139],"contigs.":[60],"propose":[62],"two":[63],"refinement":[64],"methods":[65],"to":[66,148,221],"obtain":[67],"optimal":[69],"set":[70],"contigs":[72,178,208],"representing":[73],"haplotypes.":[75],"first":[77],"method":[78],"clusters":[79],"reconstructed":[81],"VSEARCH":[85],"Deorowicz":[86],"et":[87],"al.":[88],"2015":[89],"based":[90],"on":[91,111,153],"sequence":[92],"similarity,":[93],"while":[94],"second":[96],"method,":[97],"MLEHaplo,":[98],"maximum":[101],"likelihood":[102],"estimate":[103],"populations.":[106],"evaluated":[108],"our":[109],"pipeline":[110],"both":[112],"simulated":[113],"and":[114,218],"real":[115,122,155],"quasispecies":[117],"data":[118,123],"HIV":[120,154],"(and":[121],"SARS-COV-2).":[125],"Experimental":[126],"results":[127],"show":[128],"that":[129,209],"although":[131],"still":[132],"overestimation":[134],"number":[137],"contigs,":[140],"outperforms":[141],"existing":[143],"tool,":[144],"PEHaplo,":[145],"providing":[146],"up":[147],"9%":[149],"better":[150],"genome":[151,217],"coverage":[152],"In":[157],"addition,":[158],"ViPRA-Haplo":[159,206],"also":[160,186],"retains":[161],"higher":[162,175],"diversity":[163],"as":[168],"demonstrated":[169],"presence":[172],"percentage":[176],"less":[179,191],"than":[180,192,212],"1000":[181],"base":[182],"pairs":[183],"(bps),":[184],"which":[185,197],"contain":[187],"k-mers":[188],"with":[189],"counts":[190],"100":[193],"(representing":[194],"rarer":[195],"sequences),":[196],"absent":[199],"PEHaplo.":[201],"For":[202],"SARS-CoV-2":[203,224],"data,":[205],"reconstructs":[207],"cover":[210],"more":[211],"90%":[213],"reference":[216],"were":[219],"able":[220],"validate":[222],"known":[223],"strains":[225]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
