{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T19:23:32Z","timestamp":1779391412224,"version":"3.53.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005944","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,7]],"date-time":"2018-02-07T00:00:00Z","timestamp":1517961600000}}],"reference-count":28,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T00:00:00Z","timestamp":1516924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM083873"],"award-info":[{"award-number":["R01 GM083873"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","award":["GBMF4554"],"award-info":[{"award-number":["GBMF4554"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS-1238231"],"award-info":[{"award-number":["IOS-1238231"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ABR-PG-144893"],"award-info":[{"award-number":["ABR-PG-144893"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005944","type":"journal-article","created":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T13:23:26Z","timestamp":1516973006000},"page":"e1005944","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2401,"title":["MUMmer4: A fast and versatile genome alignment system"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5083-5925","authenticated-orcid":true,"given":"Guillaume","family":"Mar\u00e7ais","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur L.","family":"Delcher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam M.","family":"Phillippy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Coston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L.","family":"Salzberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5091-3092","authenticated-orcid":true,"given":"Aleksey","family":"Zimin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,1,26]]},"reference":[{"issue":"2","key":"ref1","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biology"},{"issue":"3","key":"ref2","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"Journal of Molecular Biology"},{"issue":"3","key":"ref3","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biology"},{"issue":"14","key":"ref4","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u00e2\u20ac\u201cWheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"ref5","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1101\/gr.229202","article-title":"BLAT\u00e2\u20ac\u201dThe BLAST-Like Alignment Tool","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Research"},{"issue":"7","key":"ref6","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","article-title":"Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements","volume":"14","author":"ACE Darling","year":"2004","journal-title":"Genome Research"},{"key":"ref7","unstructured":"Harris RS. Improved pairwise alignment of genomic DNA [Ph.D.]. The Pennsylvania State University. United States\u2014Pennsylvania; 2007."},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"MJ Chaisson","year":"2012","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"ref9","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1093\/nar\/27.11.2369","article-title":"Alignment of whole genomes","volume":"27","author":"AL Delcher","year":"1999","journal-title":"Nucleic Acids Research"},{"issue":"16","key":"ref10","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"ref11","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","article-title":"Identification of common molecular subsequences","volume":"147","author":"TF Smith","year":"1981","journal-title":"Journal of Molecular Biology"},{"key":"ref12","article-title":"essaMEM: finding maximal exact matches using enhanced sparse suffix arrays","author":"M Vyverman","year":"2013","journal-title":"Bioinformatics"},{"issue":"3","key":"ref13","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.tcs.2007.07.017","article-title":"Faster suffix sorting","volume":"387","author":"NJ Larsson","year":"2007","journal-title":"Theoretical Computer Science"},{"key":"ref14","unstructured":"Mori Y. libdivsufsort: A lightweight suffix-sorting library, 2010; 2010. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/y-256\/libdivsufsort\/\" xlink:type=\"simple\">https:\/\/github.com\/y-256\/libdivsufsort\/<\/ext-link>."},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1534\/genetics.116.193227","article-title":"Sequence of the Sugar Pine Megagenome","volume":"204","author":"KA Stevens","year":"2016","journal-title":"Genetics"},{"issue":"4","key":"ref16","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature methods"},{"key":"ref17","unstructured":"Beazley DM, others. SWIG: An easy to use tool for integrating scripting languages with C and C++. In: Proceedings of the 4th USENIX Tcl\/Tk workshop; 1996. p. 129\u2013139. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.usenix.org\/legacy\/publications\/library\/proceedings\/tcl96\/full_papers\/beazley\" xlink:type=\"simple\">https:\/\/www.usenix.org\/legacy\/publications\/library\/proceedings\/tcl96\/full_papers\/beazley<\/ext-link>."},{"issue":"6814","key":"ref18","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/35048692","article-title":"Analysis of the genome sequence of the flowering plant Arabidopsis thaliana","volume":"408","author":"S Kaul","year":"2000","journal-title":"Nature"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1101\/gr.213611.116","article-title":"Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly","volume":"27","author":"VA Schneider","year":"2017","journal-title":"Genome Research"},{"issue":"7055","key":"ref20","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nature04072","article-title":"Initial sequence of the chimpanzee genome and comparison with the human genome","volume":"437","author":"T Mikkelsen","year":"2005","journal-title":"Nature"},{"issue":"5","key":"ref21","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/ng.807","article-title":"The Arabidopsis lyrata genome sequence and the basis of rapid genome size change","volume":"43","author":"TT Hu","year":"2011","journal-title":"Nature genetics"},{"key":"ref22","article-title":"Error correction and assembly complexity of single molecule sequencing reads","author":"H Lee","year":"2014","journal-title":"bioRxiv"},{"key":"ref23","unstructured":"ECtools and data;. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/schatzlab.cshl.edu\/data\/ectools\/\" xlink:type=\"simple\">http:\/\/schatzlab.cshl.edu\/data\/ectools\/<\/ext-link>."},{"key":"ref24","first-page":"026468","article-title":"Extensive sequencing of seven human genomes to characterize benchmark reference materials","author":"JM Zook","year":"2015","journal-title":"bioRxiv"},{"issue":"7055","key":"ref25","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nature04072","article-title":"Initial sequence of the chimpanzee genome and comparison with the human genome","volume":"437","author":"TS Mikkelsen","year":"2005","journal-title":"Nature"},{"issue":"52","key":"ref26","doi-asserted-by":"crossref","first-page":"15976","DOI":"10.1073\/pnas.1510461112","article-title":"Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade","volume":"112","author":"TC Boothby","year":"2015","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"18","key":"ref27","doi-asserted-by":"crossref","first-page":"5053","DOI":"10.1073\/pnas.1600338113","article-title":"No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini","volume":"113","author":"G Koutsovoulos","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1093\/bioinformatics\/bts649","article-title":"PBSIM: PacBio reads simulator\u00e2\u20ac\u201dtoward accurate genome assembly","volume":"29","author":"Y Ono","year":"2012","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005944","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,7]],"date-time":"2018-02-07T00:00:00Z","timestamp":1517961600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005944","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T15:39:51Z","timestamp":1539963591000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005944"}},"subtitle":[],"editor":[{"given":"Aaron E.","family":"Darling","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,26]]},"references-count":28,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005944","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1005944","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,26]]}}}