{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T08:45:49Z","timestamp":1775983549080,"version":"3.50.1"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,6]],"date-time":"2020-08-06T00:00:00Z","timestamp":1596672000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100020701","name":"Prime Minister\u2019s Office","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100020701","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Synthetic Biology Research and Development Programme","award":["SBP-P3"],"award-info":[{"award-number":["SBP-P3"]}]},{"name":"Kwan Im Thong Hood Cho Temple Chair Professorship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Existing genome assembly evaluation metrics provide only limited insight on specific aspects of genome assembly quality, and sometimes even disagree with each other. For better integrative comparison between assemblies, we propose, here, a new genome assembly evaluation metric, Pairwise Distance Reconstruction (PDR). It derives from a common concern in genetic studies, and takes completeness, contiguity, and correctness into consideration. We also propose an approximation implementation to accelerate PDR computation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our results on publicly available datasets affirm PDR\u2019s ability to integratively assess the quality of a genome assembly. In fact, this is guaranteed by its definition. The results also indicated the error introduced by approximation is extremely small and thus negligible.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/XLuyu\/PDR.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa704","type":"journal-article","created":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T11:29:59Z","timestamp":1596194999000},"page":"289-295","source":"Crossref","is-referenced-by-count":6,"title":["PDR: a new genome assembly evaluation metric based on genetics concerns"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3300-6401","authenticated-orcid":false,"given":"Luyu","family":"Xie","sequence":"first","affiliation":[{"name":"Department of Computer Science, School of Computing, National University of Singapore , Singapore 117417, Singapore"}]},{"given":"Limsoon","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Computer Science, School of Computing, National University of Singapore , Singapore 117417, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2020,8,6]]},"reference":[{"key":"2023051603583761500_btaa704-B1","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s13059-017-1213-3","article-title":"A comparative evaluation of genome assembly reconciliation tools","volume":"18","author":"Alhakami","year":"2017","journal-title":"Genome Biol"},{"key":"2023051603583761500_btaa704-B2","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/2047-217X-2-10","article-title":"Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species","volume":"2","author":"Bradnam","year":"2013","journal-title":"GigaScience"},{"key":"2023051603583761500_btaa704-B3","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1089\/cmb.2017.0013","article-title":"U50: anew metric for measuring assembly output based on non-overlapping, target-specific contigs","volume":"24","author":"Castro","year":"2017","journal-title":"J. Comput. Biol"},{"key":"2023051603583761500_btaa704-B4","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1101\/gr.126599.111","article-title":"Assemblathon 1: a competitive assessment of de novo short read assembly methods","volume":"21","author":"Earl","year":"2011","journal-title":"Genome Res"},{"key":"2023051603583761500_btaa704-B5","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1186\/1756-0500-6-334","article-title":"De novo likelihood-based measures for comparing genome assemblies","volume":"6","author":"Ghodsi","year":"2013","journal-title":"BMC Res. Notes"},{"key":"2023051603583761500_btaa704-B6","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"Quast: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051603583761500_btaa704-B7","doi-asserted-by":"crossref","first-page":"e24182","DOI":"10.1371\/journal.pone.0024182","article-title":"Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results","volume":"6","author":"Haiminen","year":"2011","journal-title":"PLoS One"},{"key":"2023051603583761500_btaa704-B8","doi-asserted-by":"crossref","first-page":"R47","DOI":"10.1186\/gb-2013-14-5-r47","article-title":"Reapr: a universal tool for genome assembly evaluation","volume":"14","author":"Hunt","year":"2013","journal-title":"Genome Biol"},{"key":"2023051603583761500_btaa704-B9","doi-asserted-by":"crossref","first-page":"866","DOI":"10.1093\/bib\/bbx147","article-title":"Comprehensive evaluation of non-hybrid genome assembly tools for third-generation pacbio long-read sequence data","volume":"20","author":"Jayakumar","year":"2019","journal-title":"Brief. Bioinf"},{"key":"2023051603583761500_btaa704-B10","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences","volume":"32","author":"Li","year":"2016","journal-title":"Bioinformatics"},{"key":"2023051603583761500_btaa704-B11","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051603583761500_btaa704-B12","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1186\/1471-2105-13-255","article-title":"Normalized N50 assembly metric using gap-restricted co-linear chaining","volume":"13","author":"M\u00e4kinen","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023051603583761500_btaa704-B13","doi-asserted-by":"crossref","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput. Biol"},{"key":"2023051603583761500_btaa704-B14","doi-asserted-by":"crossref","first-page":"e19175","DOI":"10.1371\/journal.pone.0019175","article-title":"Comparing de novo genome assembly: the long and short of it","volume":"6","author":"Narzisi","year":"2011","journal-title":"PLoS One"},{"key":"2023051603583761500_btaa704-B15","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/bioinformatics\/btm071","article-title":"Cegma: a pipeline to accurately annotate core genes in eukaryotic genomes","volume":"23","author":"Parra","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051603583761500_btaa704-B16","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1101\/gr.131383.111","article-title":"GAGE: a critical evaluation of genome assemblies and assembly algorithms","volume":"22","author":"Salzberg","year":"2012","journal-title":"Genome Res"},{"key":"2023051603583761500_btaa704-B17","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051603583761500_btaa704-B18","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1101\/gr.5396706","article-title":"SyMAP: a system for discovering and viewing syntenic regions of FPC maps","volume":"16","author":"Soderlund","year":"2006","journal-title":"Genome Res"},{"key":"2023051603583761500_btaa704-B19","doi-asserted-by":"crossref","first-page":"2582","DOI":"10.1093\/bioinformatics\/btw237","article-title":"Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads","volume":"32","author":"Sovi\u0107","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa704\/34127063\/btaa704.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/289\/50326135\/btaa704.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/3\/289\/50326135\/btaa704.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T03:59:40Z","timestamp":1684209580000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/3\/289\/5881632"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,6]]},"references-count":19,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2021,4,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa704","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,2,1]]},"published":{"date-parts":[[2020,8,6]]}}}