CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes

Frontiers in Microbiology

Felicita Mabel Duré¹  Rodolpho Mattos Albano²  Elizabeth Andrade Marques³  Robson Souza Leão³  Melise Chaves Silveira⁴  Ivson Cassiano de Oliveira Santos⁴  Ana Paula D’Alincourt Carvalho-Assef⁴  Cláudio Marcos Rocha-de-Souza⁴  Fabricio Alves Barbosa da Silva⁵ 

[1] Central Public Health Laboratory (LCSP), Ministry of Public Health and Social Welfare MSPyBS, Asunción, Paraguay;Department of Biochemistry, Roberto de Alcântara Gomes Biology Institute, State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil;Department of Microbiology, Immunology and Parasitology - Medical Sciences College - State University of Rio de Janeiro – UERJ, Rio de Janeiro, Brazil;Hospital Infection Research Laboratory (LAPIH), Oswaldo Cruz Institute–Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil;Scientific Computing Program–Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil;

关键词: bacteria;    web application;    pipeline;    bioinformatics;    genome;    antimicrobial resistance;   

DOI  :  10.3389/fmicb.2022.893474

来源: DOAJ

【 摘 要 】

Due to recent developments in NGS technologies, genome sequencing is generating large volumes of new data containing a wealth of biological information. Understanding sequenced genomes in a biologically meaningful way and delineating their functional and metabolic landscapes is a first-level challenge. Considering the global antimicrobial resistance (AMR) problem, investments to expand surveillance and improve existing genome analysis technologies are pressing. In addition, the speed at which new genomic data is generated surpasses our capacity to analyze it with available bioinformatics methods, thus creating a need to develop new, user-friendly and comprehensive analytical tools. To this end, we propose a new web application, CABGen,1 developed with open-source software. CABGen allows storing, organizing, analyzing, and interpreting bioinformatics data in a friendly, scalable, easy-to-use environment and can process data from bacterial isolates of different species and origins. CABGen has three modules: Upload Sequences, Analyze Sequences, and Verify Results. Functionalities include coverage estimation, species identification, de novo genome assembly, and assembly quality, genome annotation, MLST mapping, searches for genes related to AMR, virulence, and plasmids, and detection of point mutations in specific AMR genes. Visualization tools are also available, greatly facilitating the handling of biological data. The reports include those results that are clinically relevant. To illustrate the use of CABGen, whole-genome shotgun data from 181 bacterial isolates of different species collected in 5 Brazilian regions between 2018 and 2020 were uploaded and submitted to the platform’s modules.

【 授权许可】

Unknown