Use este identificador para citar ou linkar para este item: http://www.alice.cnptia.embrapa.br/alice/handle/doc/868519
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dc.contributor.authorHERAI, R. H.pt_BR
dc.contributor.authorCOSTA, G. G. D. L.pt_BR
dc.contributor.authorR. JÚNIOR, O.pt_BR
dc.contributor.authorVIDAL, R. O.pt_BR
dc.contributor.authorNASCIMENTO, L. C.pt_BR
dc.contributor.authorPARIZZI, L. P.pt_BR
dc.contributor.authorPEREIRA, G. G. A.pt_BR
dc.contributor.authorCARAZZOLLE, M. F.pt_BR
dc.date.accessioned2011-04-10T11:11:11Zpt_BR
dc.date.available2011-04-10T11:11:11Zpt_BR
dc.date.created2010-12-02pt_BR
dc.date.issued2010pt_BR
dc.identifier.citationIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010.pt_BR
dc.identifier.urihttp://www.alice.cnptia.embrapa.br/alice/handle/doc/868519pt_BR
dc.descriptionNext generation sequence technologies (NGS) made possible to sequence entirely genomes in a fast way and low cost, from unicellular to complex organisms, like plants and mammals. These sequences can be assembled (i ) using a reference genome or by some de novo bioinformatics method, such as Velvet, SOAPDenovo, Edena, ABYSS, GS Assembler 454, Mira and ZORRO. They are mainly based on de Bruijin graphs or, in a few softwares, reads overlapping to form contigs and scaffolds. The involved filtering and assembly step are very sensitive for each type of tool, and can be a key factor to generate the best assembly results. This way, when a set of sequences from distinct technologies exists, from Sanger to NGS, it is necessary the use of distinct assembly strategies for each type of data. Actually, at our knowledge, there is no automated hybrid strategies based on in-use of distinct assembly softwares that can be applied to assembly hybrid data generated by NGS or Sanger platforms. This works presents TORNADO, and automated pipeline for hybrid genome assembly based on free software packages. TORNADO did not proposed new methods for genome assembly. It just uses the best described software strategies for each type of genomic data to perform the hybrid assembly. It was organized in two main modules that are configured by XML file. In the first module, input data are filtered for trimming and experimental artifacts clipping. In the second module, based on sequence type, TORNADO automatically performs the assembly task using Mira for 454 and Sanger reads, Velvet for Illumina/Solexa or Solid/Life Tech reads. Finally, each assembled data are merged in a single assembly using ZORRO. If there are paired-end (mate pairs data) reads, an additional step involves CloseGaps software, which closes the gaps between assembled scaffolds. TORNADO was already applied to assembly hybrid genomic reads from Moniliophthora perniciosa fungi, Witche's broom causal in plant cacao. Results showed that our strategy can works like an useful method to automatically assembly hybrid genome data. TORNADO's was implemented using Java and PERL programming language technologies.pt_BR
dc.language.isoengeng
dc.rightsopenAccesseng
dc.subjectBases de dadospt_BR
dc.subjectBioinformáticapt_BR
dc.titleTORNADO: an automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS).pt_BR
dc.typeResumo em anais e proceedingspt_BR
dc.date.updated2020-01-27T11:11:11Zpt_BR
dc.subject.thesagroGenomapt_BR
dc.subject.nalthesaurusGenomept_BR
dc.subject.nalthesaurusMoniliophthora perniciosapt_BR
dc.subject.nalthesaurusDatabasespt_BR
dc.subject.nalthesaurusBioinformaticspt_BR
dc.subject.nalthesaurusComputer softwarept_BR
dc.description.notesX-meeting 2010.pt_BR
dc.format.extent2p. 119.pt_BR
riaa.ainfo.id868519pt_BR
riaa.ainfo.lastupdate2020-01-27 -02:00:00pt_BR
dc.contributor.institutionLGE/IB/UNICAMP, LBA/CNPTIA; LGE/UNICAMP; LGE/IB/UNICAMP; LGE/IB/UNICAMP, LNBio; LGE/IB/UNICAMP; LGE/IB/UNICAMP; LGE/IB/UNICAMP, LNBio; LGE/IB/UNICAMP, CENAPAD.pt_BR
Aparece nas coleções:Resumo em anais de congresso (CNPTIA)

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