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Hered"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/nbt.2198","article-title":"Performance comparison of benchtop high-throughput sequencing platforms","volume":"30","author":"NJ Loman","year":"2012","journal-title":"Nat Biotechnol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1093\/bib\/bbs015","article-title":"A survey of error-correction methods for next-generation sequencing","volume":"14","author":"X Yang","year":"2013","journal-title":"Brief Bioinform"},{"key":"ref40","unstructured":"Sequence Read Archive. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/sra\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/sra<\/ext-link>. Accessed 4 February 2013."},{"key":"ref41","unstructured":"Assembly Archive. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/Traces\/assembly\/\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/Traces\/assembly\/<\/ext-link>. Accessed 4 February 2013."},{"key":"ref42","unstructured":"AGP file. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/\" xlink:type=\"simple\">http:\/\/www.ncbi.nlm.nih.gov\/projects\/genome\/assembly\/agp\/<\/ext-link>. Accessed 4 February 2013."},{"key":"ref43","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/bib\/5.3.237","article-title":"Comparative genome assembly","volume":"5","author":"M Pop","year":"2004","journal-title":"Brief Bioinform"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e17915","DOI":"10.1371\/journal.pone.0017915","article-title":"A practical comparison of <italic>de novo<\/italic> genome assembly software tools for next-generation sequencing technologies","volume":"6","author":"W Zhang","year":"2011","journal-title":"PLoS ONE"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/bioinformatics\/btq653","article-title":"HiTEC: accurate error correction in high-throughput sequencing data","volume":"27","author":"L Ilie","year":"2011","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1181","DOI":"10.1101\/gr.111351.110","article-title":"ECHO: a reference-free short-read error correction 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Salmela","year":"2011","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/bioinformatics\/btp379","article-title":"SHREC: a short-read error correction method","volume":"25","author":"J Schroder","year":"2009","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1093\/bioinformatics\/btq468","article-title":"Reptile: representative tiling for short read error correction","volume":"26","author":"X Yang","year":"2010","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE","volume":"24","author":"M Boetzer","year":"2011","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1186\/1471-2105-11-345","article-title":"SOPRA: scaffolding algorithm for paired reads via statistical 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scaffolding with small independent mixed integer programs","volume":"27","author":"L Salmela","year":"2011","journal-title":"Bioinformatics"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1093\/bfgp\/elr035","article-title":"Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph","volume":"11","author":"Z Li","year":"2012","journal-title":"Brief Funct Genomics"},{"key":"ref59","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":"ref60","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1093\/bioinformatics\/bts280","article-title":"Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly","volume":"28","author":"H Li","year":"2012","journal-title":"Bioinformatics"},{"key":"ref61","doi-asserted-by":"crossref","unstructured":"Nagarajan N, Pop M (2010) Sequencing and genome assembly using next-generation technologies. In: Feny\u00f6 D, editor. Computational biology. Humana Press. pp. 1\u201317.","DOI":"10.1007\/978-1-60761-842-3_1"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1093\/bioinformatics\/btq151","article-title":"Correction of sequencing errors in a mixed set of reads","volume":"26","author":"L Salmela","year":"2010","journal-title":"Bioinformatics"},{"key":"ref63","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":"SL Salzberg","year":"2012","journal-title":"Genome Res"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1089\/cmb.2009.0047","article-title":"Maximum likelihood genome assembly","volume":"16","author":"P Medvedev","year":"2009","journal-title":"J Comput Biol"},{"key":"ref65","doi-asserted-by":"crossref","unstructured":"Medvedev P, Georgiou K, Myers G, Brudno M (2007) Computability of models for sequence assembly. In: Giancarlo R, Hannenhalli S, editors. Algorithms in bioinformatics. Springer Berlin Heidelberg. pp. 289\u2013301.","DOI":"10.1007\/978-3-540-74126-8_27"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/nar\/12.1Part1.307","article-title":"SEQAID: a DNA sequence assembling program based on a mathematical model","volume":"12","author":"H Peltola","year":"1984","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 2","key":"ref67","doi-asserted-by":"crossref","first-page":"ii79","DOI":"10.1093\/bioinformatics\/bti1114","article-title":"The fragment assembly string graph","volume":"21","author":"EW Myers","year":"2005","journal-title":"Bioinformatics"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"i367","DOI":"10.1093\/bioinformatics\/btq217","article-title":"Efficient construction of an assembly string graph using the FM-index","volume":"26","author":"JT Simpson","year":"2010","journal-title":"Bioinformatics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1089\/cmb.1995.2.291","article-title":"A new algorithm for DNA sequence assembly","volume":"2","author":"RM Idury","year":"1995","journal-title":"J Comput Biol"},{"issue":"Suppl 2","key":"ref70","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2164-12-S2-S8","article-title":"Evaluation of short read metagenomic assembly","volume":"12","author":"A Charuvaka","year":"2011","journal-title":"BMC Genomics"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-333","article-title":"Efficient counting of k-mers in DNA sequences using a bloom filter","volume":"12","author":"P Melsted","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1093\/bioinformatics\/btq697","article-title":"Succinct data structures for assembling large genomes","volume":"27","author":"TC Conway","year":"2011","journal-title":"Bioinformatics"},{"key":"ref73","doi-asserted-by":"crossref","unstructured":"Bowe A, Onodera T, Sadakane K, Shibuya T (2012) Succinct de Bruijn Graphs. In: Raphael B, Tang J, editors. Algorithms in bioinformatics. 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Proceedings of the 12th annual international conference on research in computational molecular biology. Singapore: Springer-Verlag. pp. 50\u201364.","DOI":"10.1007\/978-3-540-78839-3_5"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nmeth.1527","article-title":"Limitations of next-generation genome sequence assembly","volume":"8","author":"C Alkan","year":"2011","journal-title":"Nat Methods"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2105-13-166","article-title":"Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation","volume":"13","author":"G Golovko","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1093\/bioinformatics\/bts664","article-title":"VAGUE: a graphical user interface for the Velvet assembler","volume":"29","author":"DR Powell","year":"2013","journal-title":"Bioinformatics"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"e1000112","DOI":"10.1371\/journal.pbio.1000112","article-title":"Lineage-specific biology revealed by a finished genome assembly of the mouse","volume":"7","author":"DM Church","year":"2009","journal-title":"PLoS Biol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1126\/science.1197761","article-title":"The ecoresponsive genome of Daphnia pulex","volume":"331","author":"JK Colbourne","year":"2011","journal-title":"Science"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nature08696","article-title":"The sequence and de novo assembly of the giant panda genome","volume":"463","author":"R Li","year":"2010","journal-title":"Nature"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1038\/nature04338","article-title":"Genome sequence, comparative analysis and haplotype structure of the domestic dog","volume":"438","author":"K Lindblad-Toh","year":"2005","journal-title":"Nature"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/1471-2164-10-180","article-title":"Bos taurus genome assembly","volume":"10","author":"Y Liu","year":"2009","journal-title":"BMC Genomics"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/nature09687","article-title":"Comparative and demographic analysis of orang-utan genomes","volume":"469","author":"DP Locke","year":"2011","journal-title":"Nature"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1038\/nature06856","article-title":"The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)","volume":"452","author":"R Ming","year":"2008","journal-title":"Nature"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1093\/bioinformatics\/btr319","article-title":"Comparative studies of de novo assembly tools for next-generation sequencing technologies","volume":"27","author":"Y Lin","year":"2011","journal-title":"Bioinformatics"},{"key":"ref95","doi-asserted-by":"crossref","unstructured":"Huson DH, Halpern AL, Lai Z, Myers EW, Reinert K, <etal>et al<\/etal>.. (2001) Comparing assemblies using fragments and mate-pairs. \u00c5rhus, Denmark: Springer Berlin Heidelberg. pp. 294\u2013306","DOI":"10.1007\/3-540-44696-6_23"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"R55","DOI":"10.1186\/gb-2008-9-3-r55","article-title":"Genome assembly forensics: finding the elusive mis-assembly","volume":"9","author":"AM Phillippy","year":"2008","journal-title":"Genome Biol"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/1471-2164-8-278","article-title":"Validation of rice genome sequence by optical mapping","volume":"8","author":"S Zhou","year":"2007","journal-title":"BMC Genomics"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/nar\/gkn916","article-title":"Assessing the gene space in draft genomes","volume":"37","author":"G Parra","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"e17034","DOI":"10.1371\/journal.pone.0017034","article-title":"Error and error mitigation in low-coverage genome assemblies","volume":"6","author":"MJ Hubisz","year":"2011","journal-title":"PLoS ONE"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1101\/gr.096966.109","article-title":"Genome assembly quality: assessment and improvement using the neutral indel model","volume":"20","author":"S Meader","year":"2010","journal-title":"Genome Res"},{"key":"ref101","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":"D Earl","year":"2011","journal-title":"Genome Res"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"e24182","DOI":"10.1371\/journal.pone.0024182","article-title":"Evaluation of methods for <italic>de novo<\/italic> genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results","volume":"6","author":"N Haiminen","year":"2011","journal-title":"PLoS ONE"},{"key":"ref103","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":"G Narzisi","year":"2011","journal-title":"PLoS ONE"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"e31002","DOI":"10.1371\/journal.pone.0031002","article-title":"Feature-by-feature \u2013 evaluating <italic>de novo<\/italic> sequence assembly","volume":"7","author":"F Vezzi","year":"2012","journal-title":"PLoS ONE"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/bib\/bbp026","article-title":"Genome assembly reborn: recent computational challenges","volume":"10","author":"M Pop","year":"2009","journal-title":"Brief Bioinform"},{"key":"ref106","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":"KR Bradnam","year":"2013","journal-title":"Gigascience"},{"key":"ref107","unstructured":"Sommerville I (1995) Software engineering (5th ed.). Addison Wesley Longman Publishing Co., Inc. 742 p."},{"key":"ref108","doi-asserted-by":"crossref","first-page":"1036","DOI":"10.1038\/nbt.2404","article-title":"NGS analyses by visualization with Trackster","volume":"30","author":"J Goecks","year":"2012","journal-title":"Nat Biotech"},{"key":"ref109","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":"ref110","unstructured":"SAM (Sequence Alignment\/Map) format. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/samtools.sourceforge.net\/\" xlink:type=\"simple\">http:\/\/samtools.sourceforge.net\/<\/ext-link>. Accessed 16 August 2013."},{"key":"ref111","unstructured":"FASTG - An expressive representation for genome assemblies. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/fastg.sourceforge.net\/\" xlink:type=\"simple\">http:\/\/fastg.sourceforge.net\/<\/ext-link>. Accessed 27 May 2013."}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003345","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,4]],"date-time":"2019-08-04T17:19:06Z","timestamp":1564939146000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003345"}},"subtitle":[],"editor":[{"given":"Scott","family":"Markel","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,12,12]]},"references-count":111,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2013,12,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003345","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,12]]}}}