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http://hdl.handle.net/10609/97387
Title: | Evaluación y comparación de métodos de ensamblaje y binning a partir de datos metagenómicos reales |
Author: | Vergara Gómez, Andrea |
Tutor: | Guillén Montalbán, Yolanda |
Others: | Canovas Izquierdo, Javier Luis ![]() |
Abstract: | Thanks to the next generation sequencing it is possible to analyze the genes of all the microorganisms in a sample (metagenomics), without the need to cultivate them. The analysis of shotgun data represents a great challenge. Grouping sequences from different metagenomic species based on external references means that many sequences will remain unassigned, so it seems more appropriate to use the reference independent methods (binning). The objective of this study was to compare two assemblers and two binning methods with real metagenomic data. The de-novo assembly of trimmed reads was performed with two assemblers: MEGAHIT and MetaSPAdes. The performance of these assemblies was analyzed with QUAST. A catalog of unique genes was generated from the contigs and binning with Canopy and MetaBAT2 was carried out. The performance of the binning was evaluated with CheckM. A cluster of supercomputers was used and, whenever possible, jobs were executed in parallel, in order to optimize time of analysis. Regarding the assembly, better results were obtained using MetaSPAdes than MEGAHIT. Regarding the binning, Canopy generated many more bins than MetaBAT2, but the visualization of the bins showed that the results were suboptimal for both. Working in a cluster of PCs allows you to save analysis time and optimize resources. According to these data, new approaches are necessary to achieve better results: the single-sample strategy based on contigs, using complete contigs instead of genes and testing the result of multiple co-assembly for several samples. |
Keywords: | metagenomics assembly binning |
Document type: | info:eu-repo/semantics/masterThesis |
Issue Date: | 4-Jun-2019 |
Publication license: | http://creativecommons.org/licenses/by-nc-nd/3.0/es/ ![]() |
Appears in Collections: | Trabajos finales de carrera, trabajos de investigación, etc. |
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File | Description | Size | Format | |
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avergaragoTFM0619memoria.pdf | Memoria del TFM | 2,12 MB | Unknown | View/Open |
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