Publicação
Automatic reconstruction of persistent human virus sequences
| Resumo: | The increasing availability of expressive quantities of human viral sequenced samples, namely from clinical and forensic contexts, has led to the emergence of many optimized genome reconstruction tools. Although the number of new tools is steadily increasing, it is complex to identify functional and optimized tools for improved human viral genome reconstruction. By optimized we mean an equilibrium point between accuracy and computational resources as well as the features that each tool provides. In this thesis, the topic of automatic reconstruction of human viral genomes is explored, in particular persistent human viruses. Additionally, a survey on open-source computational tools (including pipelines) used for human viral genome reconstruction, identifying specific characteristics, features, similarities, and dissimilarities between these tools is provided. For quantitative comparison, an open-source reconstruction benchmark was created. The benchmark consists of the use of different human viruses with different mutation rates, contamination, mitochondrial DNA inclusion, while the sequencing process is simulated with different coverage depths. The evaluation measures include the identity, a Normalized Compression Semi-Distance, and the Normalized Relative Compression between the genomes before and after reconstruction, as well as the computational time and memory spent by each tool. Specifically, because the results show that there is not a best tool for all cases since it depends on the data characteristics, an enhanced pipeline for human DNA viral reconstruction is provided. The pipeline uses the cooperation between the reconstruction tools used in this study. It is shown that this pipeline is able to better adapt to the sample while reconstructing the viral genomes with increasing accuracy; in some cases providing a substantial increase. Moreover, this pipeline has the flexibility to turn on and off any of the used tools. The benchmark and the cooperation pipeline are fully reproducible and freely available at https://github.com/viromelab/HVRS and https://github.com/viromelab/CoopPipe, respectively. |
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| Autores principais: | Sousa, Maria João Pereira e |
| Assunto: | Human viral genomes Viral reconstruction Sequence assembly Survey Reproducibility Cooperation |
| Ano: | 2023 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade de Aveiro |
| Idioma: | inglês |
| Origem: | RIA - Repositório Institucional da Universidade de Aveiro |
| Resumo: | The increasing availability of expressive quantities of human viral sequenced samples, namely from clinical and forensic contexts, has led to the emergence of many optimized genome reconstruction tools. Although the number of new tools is steadily increasing, it is complex to identify functional and optimized tools for improved human viral genome reconstruction. By optimized we mean an equilibrium point between accuracy and computational resources as well as the features that each tool provides. In this thesis, the topic of automatic reconstruction of human viral genomes is explored, in particular persistent human viruses. Additionally, a survey on open-source computational tools (including pipelines) used for human viral genome reconstruction, identifying specific characteristics, features, similarities, and dissimilarities between these tools is provided. For quantitative comparison, an open-source reconstruction benchmark was created. The benchmark consists of the use of different human viruses with different mutation rates, contamination, mitochondrial DNA inclusion, while the sequencing process is simulated with different coverage depths. The evaluation measures include the identity, a Normalized Compression Semi-Distance, and the Normalized Relative Compression between the genomes before and after reconstruction, as well as the computational time and memory spent by each tool. Specifically, because the results show that there is not a best tool for all cases since it depends on the data characteristics, an enhanced pipeline for human DNA viral reconstruction is provided. The pipeline uses the cooperation between the reconstruction tools used in this study. It is shown that this pipeline is able to better adapt to the sample while reconstructing the viral genomes with increasing accuracy; in some cases providing a substantial increase. Moreover, this pipeline has the flexibility to turn on and off any of the used tools. The benchmark and the cooperation pipeline are fully reproducible and freely available at https://github.com/viromelab/HVRS and https://github.com/viromelab/CoopPipe, respectively. |
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