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Limits to sequencing and de novo assembly: Classic benchmark sequences for optimizing fungal NGS designs

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dc.creatorMuñoz, José Fernandospa
dc.creatorMisas, Elizabethspa
dc.creatorGallo, Juan Estebanspa
dc.creatorMcEwen, Juan Guillermospa
dc.creatorClay, Oliver Keatingespa
dc.date.accessioned2020-05-26T00:05:36Z
dc.date.available2020-05-26T00:05:36Z
dc.date.created2014spa
dc.description.abstractPlanning of pipelines for next-generation sequencing (NGS) projects could be facilitated by using simple DNA sequence benchmarks, i.e., standard test sequences that could monitor or help to predict ease or difficulty of (a) short-read sequencing and (b) de novo assembly of the sequenced reads. We propose that familiar, gene-sized sequences, including but not limited to nuclear protein-coding genes, would provide feasible consensus benchmarks allowing simple visualization. We illustrate our proposal for fungi with candidates from ribosomal DNA (rDNA, used in phylogeny and identification/diagnostics), mitochondrial DNA (mtDNA), and combinatorially constructed conceptual (synthetic) DNA sequences. The exploratory analysis of such familiar candidate loci could be a step toward finding, testing and establishing familiar, biologically interpretable consensus benchmark sequences for fungal and other eukaryotic genomes. © Springer International Publishing Switzerland 2014.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1007/978-3-319-01568-2_32
dc.identifier.issn21945357
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/23808
dc.language.isoengspa
dc.publisherSpringer Verlagspa
dc.relation.citationEndPage230
dc.relation.citationStartPage221
dc.relation.citationTitleAdvances in Intelligent Systems and Computing
dc.relation.citationVolumeVol. 232
dc.relation.ispartofAdvances in Intelligent Systems and Computing, ISSN:21945357, Vol.232,(2014); pp. 221-230spa
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84894870251&doi=10.1007%2f978-3-319-01568-2_32&partnerID=40&md5=f32e9f2c6aadbf821c64c520f22487bbspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subject.keywordBenchmarkingspa
dc.subject.keywordBiologyspa
dc.subject.keywordDNA sequencesspa
dc.subject.keywordGenesspa
dc.subject.keywordNucleic acidsspa
dc.subject.keywordDe novo assembliesspa
dc.subject.keywordEukaryotic genomespa
dc.subject.keywordExploratory analysisspa
dc.subject.keywordMitochondrial DNA (mtdna)spa
dc.subject.keywordNext-generation sequencingspa
dc.subject.keywordProtein-coding genesspa
dc.subject.keywordRibosomal DNAspa
dc.subject.keywordStandard testsspa
dc.subject.keywordBioinformaticsspa
dc.subject.keywordBenchmarkingspa
dc.subject.keywordDe novo assemblyspa
dc.subject.keywordEukaryotic genomesspa
dc.subject.keywordNext generation sequencingspa
dc.titleLimits to sequencing and de novo assembly: Classic benchmark sequences for optimizing fungal NGS designsspa
dc.typeconferenceObjecteng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaDocumento de conferenciaspa
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