Análise comparativa de ferramentas de Montagem e Binning de metagenomas utilizando dados simulados microbianos
Resumo
Binning consiste em agrupar sequências de DNA de acordo com unidades taxonômicas, muito usado na Metagenômica, campo que estuda o genoma de comunidades de microrganismos. Novas ferramentas são desenvolvidas para pipelines metagenômicos, necessitando que se estabeleçam paradigmas neste tipo de análise através da verificação do desempenho de ferramentas de montagem e binning. Para os testes comparativos deste trabalho foram utilizados conjuntos de dados de 10 e 100 espécies de bactérias, além de 3 softwares montadores: IDBA_UD, Megahit e MetasSPAdes, e 2 softwares de binning: MetaBAT-2.12.1 e MaxBin-2.2.4. Verificou-se que o MetaBAT superou o MaxBin na qualidade dos bins gerados.
Referências
IMELFORT, M. et al. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, v. 2, p. e603, 2014.
KANG, D. D. et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, v. 3, p. e1165, 2015.
LANGMEAD, B.; SALZBERG, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods, v. 9, n.4, p. 357–359, 2012.
MENDE, D. R. et al. Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data. PLos ONE v. 7, n. 2, 2012.
MIKHEENKO, A.; SAVELIEV, V.; GUREVICH, A. MetaQUAST: Evaluation of metagenome assemblies. Bioinformatics, v. 32, n. 7, 2016.
NAMIKI, T. et al. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Research, v. 40, n. 20, 2012.
NURK, S et al. MetaSPades: a new versatile metagenomics assembler Sergey. Genome Research, v. 27, n. 5, p. 824-834, 2017.
PENG, Y. et al. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics, v. 27, p. 94–101, 2011.
SCHMIEDER, R.; EDWARDS, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics, v. 27, n. 6, p. 863–864, 2011.
SHARPTON, T. J. An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science, v. 5, p. 1–14, 2014.
WOOLEY, J. C.; GODZIK, A.; FRIEDBERG, I. A Primer on Metagenomics. PLoS Computational Biology, v. 6, n. 2, 2010.
KANG, D. D. et al. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, v. 3, p. e1165, 2015.
LANGMEAD, B.; SALZBERG, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods, v. 9, n.4, p. 357–359, 2012.
MENDE, D. R. et al. Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data. PLos ONE v. 7, n. 2, 2012.
MIKHEENKO, A.; SAVELIEV, V.; GUREVICH, A. MetaQUAST: Evaluation of metagenome assemblies. Bioinformatics, v. 32, n. 7, 2016.
NAMIKI, T. et al. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Research, v. 40, n. 20, 2012.
NURK, S et al. MetaSPades: a new versatile metagenomics assembler Sergey. Genome Research, v. 27, n. 5, p. 824-834, 2017.
PENG, Y. et al. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics, v. 27, p. 94–101, 2011.
SCHMIEDER, R.; EDWARDS, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics, v. 27, n. 6, p. 863–864, 2011.
SHARPTON, T. J. An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science, v. 5, p. 1–14, 2014.
WOOLEY, J. C.; GODZIK, A.; FRIEDBERG, I. A Primer on Metagenomics. PLoS Computational Biology, v. 6, n. 2, 2010.
Publicado
24/06/2019
Como Citar
PARÁ, Rodrigo B. P. R.; ROCHA, Pedro H. D. M.; COUTO, Danielle C. C.; OLIVEIRA, Renato R. M.; KAWASAKI, Regiane.
Análise comparativa de ferramentas de Montagem e Binning de metagenomas utilizando dados simulados microbianos. In: BRAZILIAN E-SCIENCE WORKSHOP (BRESCI), 13. , 2019, Belém.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2019
.
ISSN 2763-8774.
DOI: https://doi.org/10.5753/bresci.2019.10034.
