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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
02/12/2010 |
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Data da última atualização: |
27/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
HERAI, R. H.; COSTA, G. G. D. L.; R. JÚNIOR, O.; VIDAL, R. O.; NASCIMENTO, L. C.; PARIZZI, L. P.; PEREIRA, G. G. A.; CARAZZOLLE, M. F. |
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Afiliação: |
LGE/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. |
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Título: |
TORNADO: an automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS). |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. |
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Páginas: |
p. 119. |
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Idioma: |
Inglês |
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Notas: |
X-meeting 2010. |
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Conteúdo: |
Next 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. MenosNext 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 automatic... Mostrar Tudo |
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Palavras-Chave: |
Bases de dados; Bioinformática. |
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Thesagro: |
Genoma. |
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Thesaurus Nal: |
Bioinformatics; Computer software; Databases; Genome; Moniliophthora perniciosa. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/23820/1/p119.pdf
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Marc: |
LEADER 03245nam a2200313 a 4500
001 1868519
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008 2010 bl uuuu u00u1 u #d
100 1 $aHERAI, R. H.
245 $aTORNADO$ban automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS).$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010.$c2010
300 $ap. 119.
500 $aX-meeting 2010.
520 $aNext 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.
650 $aBioinformatics
650 $aComputer software
650 $aDatabases
650 $aGenome
650 $aMoniliophthora perniciosa
650 $aGenoma
653 $aBases de dados
653 $aBioinformática
700 1 $aCOSTA, G. G. D. L.
700 1 $aR. JÚNIOR, O.
700 1 $aVIDAL, R. O.
700 1 $aNASCIMENTO, L. C.
700 1 $aPARIZZI, L. P.
700 1 $aPEREIRA, G. G. A.
700 1 $aCARAZZOLLE, M. F.
Download
Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Biblioteca |
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Tipo/Formato |
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Registro |
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| Registros recuperados : 14 | |
| 1. |  | MARTINATI, J. C.; CARDOSO, D. C.; GUERREIRO-FILHO, O.; VIDAL, R. O.; CARAZZOLLE, M. F.; MALUF, M. P. Caracterização molecular da interação cafeeiro/bicho-mineiro. In: SIMPÓSIO DE PESQUISA DOS CAFÉS DO BRASIL, 7., 2011, Araxá. Anais... Brasília, DF: Embrapa Café, 2011.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Café. |
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| 2. | | HERAI, R. H.; VIDAL, R. O.; CARAZZOLLE, M. F.; COSTA, G. G. L.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; FRANCHINI, K. G.; PEREIRA, G. G. A. CNBi: the new Brazilian National Consortium for Bioinformatics. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. p. 110. X-meeting 2010.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 3. | | VIDAL, R. O.; ALEKCEVETCH, J. C.; LEROY, T.; DE BELLIS, F.; POT, D.; RODRIGUES, G. C.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; ANDRADE, A. C.; MARRACCINI, P. High-through put sequencing of CDNA shows that CV. Rubi and IAPAR59 of Coffea Arabica have different molecular response to water privation. In: INTERNATIONAL CONFERENCE ON COFFEE SCIENCE, 2012, San José. Proceedings... [S.l]: Association for Science and Information on Coffee (ASIC), 2012. p. 61.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Recursos Genéticos e Biotecnologia. |
|  |
| 4. | | MARTINATI, J. C.; CARDOSO, D. C.; VIDAL, R. O.; CARAZZOLLE, M. F.; GIACHETTO, P. F.; PADILHA, L.; GUERREIRO-FILHO, O.; MALUF, M. P. Large-escale expression of genes related to phytoalexins, phenols, flavonoids and lignin biosynthesis in coffee plants infested with leaf-miner. In: INTERNATIONAL CONFERENCE ON COFFEE SCIENCE, 24., 2012, Costa Rica. Programme & abstracts. [S.l.]: Association for Science and Information on Coffee, 2012. p. 83. B11. ASIC 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 5. | | MARTINATI, J. C.; CARDOSO, D. C.; VIDAL, R. O.; CARAZZOLLE, M. F.; GIACHETTO, P. F.; PADILHA, L.; OLIVEIRA FILHO, G.; MALUF, M. P. Large-escale expression of genes related to phytoalexins, phenols, flavonoids and lignin biosynthesis in coffee plants infested with leaf-miner. In: INTERNATIONAL CONFERENCE ON COFFEE SCIENCE, 24., 2012, Costa Rica. Programme & abstracts. [S.l.]: Association for Science and Information on Coffee, 2012. p. 83 B11. ASIC 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Café. |
| |
| 6. | | CARDOSO, D. C.; MARTINATI, J. C.; GIACHETTO, P. F.; VIDAL, R. O.; CARAZZOLLE, M. F.; PADILHA, L.; GUERREIRO-FILHO, O.; MALUF, M. P. Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner-toward the identification of candidate genes for marker assisted-selection. BMC Genomics, London, v. 15, p. 1-20, 2014.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Café. |
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| 7. | | HERAI, R. H.; COSTA, G. G. D. L.; R. JÚNIOR, O.; VIDAL, R. O.; NASCIMENTO, L. C.; PARIZZI, L. P.; PEREIRA, G. G. A.; CARAZZOLLE, M. F. TORNADO: an automated pipeline for de novo hybrid genome assembly based on free software packages for sanger and next generation sequencing technologies (NGS). In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. p. 119. X-meeting 2010.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 8. | | NASCIMENTO, L. C.; COSTA, G. G. L.; VIDAL, R. O.; MEYER, L.; BINNECK, E.; KIDO, E. A.; RODRIGUES, F.; KULCHESKI, F. R.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F. Bioinformatics analysis applied to genosoja project. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book ... Rio de Janeiro: AB3C, 2009. p. 22. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 9. | | MONDEGO, J. M. C.; VIDAL, R. O.; CARAZZOLLE, M. F.; TOKUDA, E. K.; PARIZZI, L. P.; COSTA, G. G. L.; PEREIRA, L. F. P.; ANDRADE, A. C.; COLOMBO, C. A.; VIEIRA, L. G. E.; PEREIRA, G. A. G. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biology, v.11, n. 30, 2011.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Café; Embrapa Recursos Genéticos e Biotecnologia. |
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| 10. | | NASCIMENTO, L. C.; VIDAL R. O.; MONDEGO, J. M. C.; COSTA, G. G. L.; JUNIOR, O. R.; RODRIGUES, F.; NEPOMUCENO, A. L.; MARCELINO-GUIMARÃES, F. C.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F. Genotipagem de cultivares brasileiros de soja através da detecção de SNPs. In: CONGRESSO BRASILEIRO DE SOJA, 6., 2012, Cuiabá. Soja: integração nacional e desenvolvimento sustentável: resumos. Brasília, DF: Embrapa, 2012. p. 15, res. 8.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 11. | | NASCIMENTO, L. C.; VIDAL R. O.; MONDEGO, J. M. C.; COSTA, G. G. L.; JUNIOR, O. R.; RODRIGUES, F.; NEPOMUCENO, A. L.; MARCELINO-GUIMARÃES, F. C.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F. Genotipagem de cultivares brasileiros de soja através da detecção de SNPs. In: CONGRESSO BRASILEIRO DE SOJA, 6., 2012, Cuiabá. Soja: integração nacional e desenvolvimento sustentável: anais. Brasília, DF: Embrapa, 2012. 4 p. 1 CD-ROM.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 12. | | VIDAL, R. O.; MONDEGO, J. M. C.; POT, D.; AMBRÓSIO, A. B.; ANDRADE, A. C.; PEREIRA, L. F. P.; COLOMBO, C. A.; VIEIRA, L. G. E.; CARAZZOLLE, M. F.; PEREIRA, G. A. G. A high-throughput data mining of single nucleotide polymorphisms in Coffea species expresed sequence tags suggests differential homeologous gene expression in the allotetrapoloid Coffea arabica. PLANT PHYSIOLOGY, v. 154, p. 1053-1066. 2010. 1053-1066| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Café; Embrapa Recursos Genéticos e Biotecnologia. |
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| 13. | | MOFATTO, L. S.; CARNEIRO, F. de A.; VIEIRA, N. G.; DUARTE, K. E.; VIDAL, R. O.; ALEKCEVETCH, J. C.; COTTA, M. G.; VERDEIL, J-L.; LAPEYRE-MONTES, F.; LARTAUD, M.; LEROY, T.; DE BELLIS, F.; POT, D; RODRIGUES, G. C.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; ANDRADE, A. C.; MARRACCINI, P. Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. BMC Plant Biology, v. 16, n. 94, p. 1-18, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Café. |
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| 14. | | MONDEGO, J. M. C.; CARAZZOLLE, M. F.; COSTA, G. G. L.; FORMIGHIERI, E. F.; PARIZZI, L. P.; RINCONES, J.; COTOMACCI, C.; CARRARO, D. M.; CUNHA, A. F.; CARRER, H.; VIDAL, R. O.; ESTRELA, R. C.; GARCÍA, O.; THOMAZELLA, D. P. T.; OLIVEIRA, B. V.; PIRES, A. B. L.; RIO, M. C. S.; ARAÚJO, M. R. R.; CASTRO, A. L. B.; GRAMACHO, K. P.; GONÇALVES, M. S.; GÓES NETO, A.; BARBOSA, L. V.; GUILTINAM, M.; BAILEY, B.; MEINHARDT, L. W.; CASCARDO, J. C. M.; PEREIRA, G. A. G. The genome survey of Moniliophthora perniciosa, the causal agent of cacao witches' broom disease, gives insights about novel phytopathogenicity mechanisms. In: CONGRESSO BRASILEIRO DE GENÉTICA, 54., 2008, Salvador. Resumos... Salvador: SBG, 2008. 1 CD-ROM.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 14 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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