Recovery of high-quality MAGs in time-serial metagenomic data and FixAME development: an assisting curation tool of genomic assembly error
On a daily based, there is a huge amount of biological data being generated that brings deeper insight into our world. This exponential growth of information has brought many challenges, especially when dealing with metagenomic data. Thousands of metagenomic-assembled genomes (MAG) are recovered ann...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2022 |
| País: | Brasil |
| Institución: | Universidade de São Paulo (USP) |
| Repositorio: | Biblioteca Digital de Teses e Dissertações da USP |
| Idioma: | inglés |
| OAI Identifier: | oai:teses.usp.br:tde-19072022-153242 |
| Acceso en línea: | https://www.teses.usp.br/teses/disponiveis/95/95131/tde-19072022-153242/ |
| Access Level: | acceso abierto |
| Palabra clave: | Bioinformática Bioinformatics Curadoria Curation Ferramenta Genoma Genome Metagenome Metagenomica Microbiologia Microbiology Tool |
| Sumario: | On a daily based, there is a huge amount of biological data being generated that brings deeper insight into our world. This exponential growth of information has brought many challenges, especially when dealing with metagenomic data. Thousands of metagenomic-assembled genomes (MAG) are recovered annually, and many methods try to achieve the best output possible through assembly and binning approaches. But the question that every time is more frequent is: Are these MAGs reliable? The importance of having good quality data is undeniable. Retrieving reliable and complete, or nearly-complete MAGs, provides important data for further analysis and research purposes. Within this scenario, we\'d like to know if it is possible to improve the MAGs metrics quality when compared to the state-of-the art in time series data. In addition, we\'d like to develop a tool capable of locating and fixing assembly errors, thereby assisting in genomic curation. Here, we describe an approach of MAGs recovery from time-serial data called the \"screening method\", drastically reducing the recovery from potentially unreliable MAGs. In addition, we present FixAME, a tool capable of helping curate assembled sequences of metagenome, single genome, a set of bins, phages, archaea, or any organism that contains single double-stranded DNA. |
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