Congresso Brasileiro de Microbiologia 2023

Congresso Brasileiro de Microbiologia 2023

Resumo: 698-1

698-1

DEVELOPMENT OF A WEB TOOL FOR ASSEMBLING METAGENOMIC DATA AND PERFORMING FUNCTIONAL ANALYSES.

Autores:

Victor Benedito Costa Ferreira (UFPA - Federal University of Pará) ; Carlos Willian Dias Dantas (UFMG - Federal University of Minas Gerais) ; Sandy Ingrid Aguiar Alves (UFPA - Federal University of Pará) ; Denison Luiz Oliveira Moraes (UFPA - Federal University of Pará) ; David Tavares Martins (UFPA - Federal University of Pará) ; Thais Azevedo Cardoso (UFPA - Federal University of Pará) ; Valéria Alves Chaves (UFPA - Federal University of Pará) ; Artur Pedro Martins Neto (UFPA - Federal University of Pará) ; Artur Luiz da Costa da Silva (UFPA - Federal University of Pará) ; Oscar Victor Cardenas Alegria (UFPA - Federal University of Pará) ; Rommel Thiago Jucá Ramos (UFPA - Federal University of Pará, UFMG - Federal University of Minas Gerais)

Resumo:

Metagenomics is the study of the genomes of all organisms present in a specific environment, known as the metagenome. The advancement of High Throughput Sequencing (HTS) techniques has made metagenomic data acquisition more accessible. Additionally, metagenomics can be utilized for several applications such as resistance genes identification, discovering new species, and developing biotechnological products. Metagenomic analysis generates a vast amount of data, requiring the use of bioinformatics tools for processing and analysis. Despite the existence of several tools, many of them require computational expertise and have limitations, such as processing small sample sizes. Therefore, the objective of this study is to present Speedy Pipe4Meta (SP4M), a web tool for metagenomic data assembly and functional, taxonomic, and antimicrobial resistance analysis. Initially, a pipeline was developed to automate the steps of metagenomic data analysis. The steps include: (i) Quality and pre-processing using FastQC v0.11.5 and Trimmomatic v0.39; (ii) Data assembly using three assemblers, namely metaSPAdes v3.15.5, IDBA v1.1.3, and MegaHIT v1.2.9. The assemblies are evaluated with MetaQuast v5.0.2. A Python script is used to select the best assembly based on N50 value, L50 value, and total contigs, and generate bins using Maxbin v2.2.7; (iii) Taxonomic classification using Kraken2; (iv) Annotation with Prokka v1.14.6; (v) Resistance analysis using Megares v3. The pipeline is implemented using Snakemake v7.22. For the front-end interface, HTML5, CSS3, and JavaScript languages are utilized with Bootstrap v5.0 framework, and jQuery v3.6 and Altair v4.2.2 libraries for chart rendering. The back-end utilizes Django v4.1.7. Based on the identified gaps, a tool called Speedy Pipe4Meta (SP4M) was developed with the aim of simplifying metagenomic analysis for researchers without bioinformatics experience. The tool allows the submission of metagenomic reads in compressed .fastq format and performs pre-processing of this data to ensure quality and reliability of the analyses. It accomplishes metagenomic data assembly using three assembly programs. It also performs taxonomic classification of sequences, allowing identification of organisms present in the samples, and functional analysis of metagenomic sequences, enabling the identification of biological and metabolic functions present in the samples, including antimicrobial resistance analysis. Additionally, the developed tool possesses a user-friendly and interactive results visualization interface. In conclusion, the tool encompasses the steps of processing data from sequencing, data assembly and performing functional, taxonomic and antimicrobial resistance analyzes through an intuitive web interface. The results obtained with the tool offer valuable information for researchers, even for those who are not familiar with bioinformatics.

Palavras-chave:

Metagenomics, Web tool, Bioinformatic