Banca de QUALIFICAÇÃO: JULIO CESAR DA SILVA FILHO

Uma banca de QUALIFICAÇÃO de MESTRADO foi cadastrada pelo programa.
STUDENT : JULIO CESAR DA SILVA FILHO
DATE: 05/02/2026
TIME: 09:30
LOCAL: Online
TITLE:

Mitomine and Amazon AquaBio: A Computational Workflow for Automating the Assembly and Annotation of Mitogenomes and a Web Platform for Conservation and Visual Comparison of Amazonian Data

KEY WORDS:

Mitochondrial DNA, workflows, data mining, public genomic data, web data visualization, automation.

PAGES: 101
BIG AREA: Ciências Biológicas
AREA: Biofísica
SUBÁREA: Biofísica Molecular
SUMMARY:

The Next-Generation Sequencing (NGS) revolution has resulted in an explosion of genomic data in public repositories over the last decades, such as the Sequence Read Archive (SRA). However, the capacity to transform this "data deluge" into biological knowledge has not kept pace, requiring new study and analysis approaches for more efficient interpretations. Given this scenario, this research proposes an integrated computational architecture to address data dispersion and the lack of reproducibility in organelle genomics. To this end, Mitomine was developed, an automated pipeline orchestrated in Nextflow, which integrates seed-based assembly tools (NOVOPlasty) and hybrid circularization (Unicycler) to recover complete mitochondrial genomes from public whole genome sequencing (WGS) data. Additionally, a set of Python and Shell scripts was implemented for the automation of functional annotation and the generation of genomic analyses (RSCU, strand bias, and synteny). Finally, to ensure adherence to FAIR principles (Findable, Accessible, Interoperable, Reusable) and data longevity, the Amazon AquaBio platform was developed. It is a static web application (Serverless) hosted via GitHub Pages, acting as a persistence repository and interactive visualization tool. The architecture was validated through a case study with the Cichlidae family, processing raw data from 34 Amazonian species, resulting in the assembly and dissemination of 100 curated mitogenomes. The results demonstrate that the combination of container orchestration and client-side web visualization democratizes access to genomics, offering a low-cost and highly reproducible solution for the study of biodiversity in the Global South.

COMMITTEE MEMBERS:
Presidente - 2170415 - Jorge Estefano de Santana Souza
Interna - 1365498 - BEATRIZ STRANSKY FERREIRA
Interno - 3063244 - TETSU SAKAMOTO