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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 03238nam a2200313 a 4500
001 1868519
005 2020-01-27
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 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.]$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.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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Registro Completo
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Biblioteca(s): |
Embrapa Tabuleiros Costeiros. |
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Data corrente: |
04/08/2021 |
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Data da última atualização: |
17/09/2021 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 2 |
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Autoria: |
SANTOS, P. S.; FREITAS, L. dos S.; MUNIZ, E. N.; SANTANA, J. G. S.; SILVA, A. V. C. da. |
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Afiliação: |
PRISCILLA SANTANA SANTOS, UFS; LISIANE DOS SANTOS FREITAS, UFS; EVANDRO NEVES MUNIZ, CPATC; JOSEFA GRASIELA SILVA SANTANA, UENF; ANA VERUSKA CRUZ DA SILVA, CPATC. |
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Título: |
Phytochemical and antioxidant composition in accessions of the mangaba active germplasm bank. |
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Ano de publicação: |
2021 |
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Fonte/Imprenta: |
Revista Caatinga, v. 34, n. 1, p. 228-235, jan./mar. 2021. |
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DOI: |
http://dx.doi.org/10.1590/1983-21252021v34n123rc |
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Idioma: |
Inglês |
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Thesagro: |
Banco de Germoplasma; Fruta Tropical; Germoplasma; Hancornia Speciosa; Mangaba; Melhoramento Genético Vegetal. |
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Thesaurus NAL: |
Forest genetics; Germplasm; Germplasm conservation; Plant genetics; Tropical and subtropical fruits. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/224807/1/Caatinga-mangaba-2021.pdf
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Marc: |
LEADER 00962naa a2200301 a 4500
001 2133220
005 2021-09-17
008 2021 bl uuuu u00u1 u #d
024 7 $ahttp://dx.doi.org/10.1590/1983-21252021v34n123rc$2DOI
100 1 $aSANTOS, P. S.
245 $aPhytochemical and antioxidant composition in accessions of the mangaba active germplasm bank.$h[electronic resource]
260 $c2021
650 $aForest genetics
650 $aGermplasm
650 $aGermplasm conservation
650 $aPlant genetics
650 $aTropical and subtropical fruits
650 $aBanco de Germoplasma
650 $aFruta Tropical
650 $aGermoplasma
650 $aHancornia Speciosa
650 $aMangaba
650 $aMelhoramento Genético Vegetal
700 1 $aFREITAS, L. dos S.
700 1 $aMUNIZ, E. N.
700 1 $aSANTANA, J. G. S.
700 1 $aSILVA, A. V. C. da
773 $tRevista Caatinga$gv. 34, n. 1, p. 228-235, jan./mar. 2021.
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