{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T12:17:19Z","timestamp":1782389839561,"version":"3.54.5"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,19]],"date-time":"2014-11-19T00:00:00Z","timestamp":1416355200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0112963","type":"journal-article","created":{"date-parts":[[2014,11,20]],"date-time":"2014-11-20T04:36:01Z","timestamp":1416458161000},"page":"e112963","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":8857,"title":["Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement"],"prefix":"10.1371","volume":"9","author":[{"given":"Bruce J.","family":"Walker","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Abeel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrance","family":"Shea","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margaret","family":"Priest","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amr","family":"Abouelliel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharadha","family":"Sakthikumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina A.","family":"Cuomo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiandong","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Wortman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah K.","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashlee M.","family":"Earl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1038\/ng.2895","article-title":"Dense genomic sampling identifies highways of pneumococcal recombination","volume":"46","author":"C Chewapreecha","year":"2014","journal-title":"Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/ng.2744","article-title":"Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans","volume":"45","author":"I Comas","year":"2013","journal-title":"Nat Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/ng.2625","article-title":"Population genomics of post-vaccine changes in pneumococcal epidemiology","volume":"45","author":"NJ Croucher","year":"2013","journal-title":"Nat Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1016\/S1473-3099(13)70693-5","article-title":"Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study","volume":"14","author":"YH Grad","year":"2014","journal-title":"Lancet Infect Dis"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"i188","DOI":"10.1093\/bioinformatics\/bts219","article-title":"SEQuel: improving the accuracy of genome assemblies","volume":"28","author":"R Ronen","year":"2012","journal-title":"Bioinformatics"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1038\/nprot.2012.068","article-title":"A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs","volume":"7","author":"MT Swain","year":"2012","journal-title":"Nat Protoc"},{"key":"ref7","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":"M Hunt","year":"2013","journal-title":"Genome Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2105-14-S7-S6","article-title":"GAM-NGS: genomic assemblies merger for next generation sequencing","volume":"14","author":"R Vicedomini","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref9","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"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1093\/bib\/bbs086","article-title":"A survey of tools for variant analysis of next-generation genome sequencing data","volume":"15","author":"S Pabinger","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1756-0500-1-110","article-title":"Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments","volume":"1","author":"A Cubillos-Ruiz","year":"2008","journal-title":"BMC Res Notes"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e1003345","DOI":"10.1371\/journal.pcbi.1003345","article-title":"Next-generation sequence assembly: four stages of data processing and computational challenges","volume":"9","author":"S El-Metwally","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1126\/science.1061217","article-title":"Complete genome sequence of a virulent isolate of Streptococcus pneumoniae","volume":"293","author":"H Tettelin","year":"2001","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2010-11-4-r41","article-title":"Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps","volume":"11","author":"IJ Tsai","year":"2010","journal-title":"Genome Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2105-13-S14-S8","article-title":"GapFiller: a de novo assembly approach to fill the gap within paired reads","volume":"13","author":"F Nadalin","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1093\/bioinformatics\/btq269","article-title":"Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology","volume":"26","author":"TD Otto","year":"2010","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/sj.emboj.7600490","article-title":"Solution structure of choline binding protein A, the major adhesin of Streptococcus pneumoniae","volume":"24","author":"R Luo","year":"2005","journal-title":"EMBO J"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"4720","DOI":"10.1128\/IAI.67.9.4720-4724.1999","article-title":"Pneumococcal surface protein A inhibits complement activation by Streptococcus pneumoniae","volume":"67","author":"AH Tu","year":"1999","journal-title":"Infect Immun"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/nature08064","article-title":"Evolution of pathogenicity and sexual reproduction in eight Candida genomes","volume":"459","author":"G Butler","year":"2009","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"7329","DOI":"10.1073\/pnas.0401648101","article-title":"The diploid genome sequence of Candida albicans","volume":"101","author":"T Jones","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"R97","DOI":"10.1186\/gb-2013-14-9-r97","article-title":"Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure","volume":"14","author":"D Muzzey","year":"2013","journal-title":"Genome Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"6","author":"K Chen","year":"2009","journal-title":"Nat Methods"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1093\/bioinformatics\/bts566","article-title":"CLEVER: clique-enumerating variant finder","volume":"28","author":"T Marschall","year":"2012","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e26038","DOI":"10.1371\/journal.pone.0026038","article-title":"Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region","volume":"7","author":"B Weiner","year":"2012","journal-title":"PLoS One"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"3645","DOI":"10.1128\/JB.00166-10","article-title":"Variation among genome sequences of H37Rv strains of Mycobacterium tuberculosis from multiple laboratories","volume":"192","author":"TR Ioerger","year":"2010","journal-title":"J Bacteriol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"7113","DOI":"10.1093\/nar\/gks465","article-title":"Comparative genomic and proteomic analyses of PE\/PPE multigene family of Mycobacterium tuberculosis H<sub>37<\/sub>Rv and H<sub>37<\/sub>Ra reveal novel and interesting differences with implications in virulence","volume":"40","author":"S Kohli","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e40890","DOI":"10.1371\/journal.pone.0040890","article-title":"Conserved immune recognition hierarchy of mycobacterial PE\/PPE proteins during infection in natural hosts","volume":"7","author":"HM Vordermeier","year":"2012","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/0962-8479(95)90533-2","article-title":"IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, south India","volume":"76","author":"S Das","year":"1995","journal-title":"Tuber Lung Dis"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"7838","DOI":"10.1128\/JB.00827-08","article-title":"Frequent homologous recombination events in Mycobacterium tuberculosis PE\/PPE multigene families: potential role in antigenic variability","volume":"190","author":"A Karboul","year":"2008","journal-title":"J Bacteriol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.tube.2011.11.003","article-title":"Mycobacterium tuberculosis\u2014heterogeneity revealed through whole genome sequencing","volume":"92","author":"C Ford","year":"2012","journal-title":"Tuberculosis (Edinb)"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e30593","DOI":"10.1371\/journal.pone.0030593","article-title":"Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints","volume":"7","author":"CRE McEvoy","year":"2012","journal-title":"PLoS One"},{"key":"ref34","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":"Nat Methods"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e12","DOI":"10.1093\/nar\/gkr995","article-title":"GenomeView: a next-generation genome browser","volume":"40","author":"T Abeel","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"R51","DOI":"10.1186\/gb-2013-14-5-r51","article-title":"Characterizing and measuring bias in sequence data","volume":"14","author":"MG Ross","year":"2013","journal-title":"Genome Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1073\/pnas.1121491109","article-title":"Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011","volume":"109","author":"YH Grad","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2270","DOI":"10.1101\/gr.141515.112","article-title":"Finished bacterial genomes from shotgun sequence data","volume":"22","author":"FJ Ribeiro","year":"2012","journal-title":"Genome Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1101\/gr.138925.112","article-title":"Paired-end sequencing of Fosmid libraries by Illumina","volume":"22","author":"LJS Williams","year":"2012","journal-title":"Genome Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1073\/pnas.1017351108","article-title":"High-quality draft assemblies of mammalian genomes from massively parallel sequence data","volume":"108","author":"S Gnerre","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","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":"J Mol Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1093\/nar\/30.11.2478","article-title":"Fast algorithms for large-scale genome alignment and comparison","volume":"30","author":"AL Delcher","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"a Larkin M","year":"2007","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1111\/j.1574-6968.1999.tb13575.x","article-title":"BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences","volume":"174","author":"TA Tatusova","year":"1999","journal-title":"FEMS Microbiol Lett"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"i24","DOI":"10.1093\/bioinformatics\/btn172","article-title":"ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles","volume":"24","author":"T Abeel","year":"2008","journal-title":"Bioinformatics"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0112963","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,27]],"date-time":"2020-08-27T01:18:46Z","timestamp":1598491126000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0112963"}},"subtitle":[],"editor":[{"given":"Junwen","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,11,19]]},"references-count":46,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0112963","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,19]]}}}