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Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/ruanjue\/wtdbg\" xlink:type=\"simple\">https:\/\/github.com\/ruanjue\/wtdbg<\/ext-link>."},{"issue":"14","key":"ref26","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1093\/bioinformatics\/btw152","article-title":"Minimap and miniasm: fast mapping and <italic>de novo<\/italic> assembly for noisy long sequences","volume":"32","author":"H Li","year":"2016","journal-title":"Bioinformatics"},{"issue":"11","key":"ref27","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PLOS One"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/s12864-018-4567-3","article-title":"P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads","volume":"19","author":"B-H Zhu","year":"2018","journal-title":"BMC Genomics"},{"issue":"8","key":"ref29","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"14","key":"ref30","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":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"16","key":"ref31","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"},{"issue":"19","key":"ref32","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":"FA Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"issue":"10","key":"ref33","doi-asserted-by":"crossref","first-page":"e68","DOI":"10.1093\/nar\/gkr123","article-title":"SyMAP v3.4: a turnkey synteny system with application to plant genomes","volume":"39","author":"C Soderlund","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.molbiopara.2016.11.005","article-title":"WormBase ParaSite \u2212 a comprehensive resource for helminth genomics","volume":"215","author":"KL Howe","year":"2017","journal-title":"Mol Biochem Parasitol"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"4.10.1","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"M Tarailo\u2010Graovac","year":"2009","journal-title":"Curr Protoc Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"W Bao","year":"2015","journal-title":"Mobile DNA"},{"key":"ref37","unstructured":"Smit A, Hubley R. RepeatModeler-1.0. 5 2012. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.repeatmasker.org\/RepeatModeler\/\" xlink:type=\"simple\">http:\/\/www.repeatmasker.org\/RepeatModeler\/<\/ext-link>."},{"issue":"suppl_2","key":"ref38","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkl200","article-title":"AUGUSTUS: ab initio prediction of alternative transcripts","volume":"34","author":"M Stanke","year":"2006","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"I Korf","year":"2004","journal-title":"BMC Bioinformatics"},{"issue":"suppl_2","key":"ref40","doi-asserted-by":"crossref","first-page":"W451","DOI":"10.1093\/nar\/gki487","article-title":"GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses","volume":"33","author":"J 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Haas","year":"2008"},{"issue":"1","key":"ref51","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/1471-2164-7-327","article-title":"Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis","volume":"7","author":"MA Campbell","year":"2006","journal-title":"BMC Genomics"},{"issue":"8","key":"ref52","doi-asserted-by":"crossref","first-page":"R93","DOI":"10.1186\/gb-2013-14-8-r93","article-title":"Web Apollo: a web-based genomic annotation editing platform","volume":"14","author":"E Lee","year":"2013","journal-title":"Genome Biol"},{"issue":"8","key":"ref53","doi-asserted-by":"crossref","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"M Lawrence","year":"2013","journal-title":"PLoS Comp Biol"},{"issue":"5","key":"ref54","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.0955","article-title":"tRNAscan-SE: a 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