International Journal of Science, Engineering and TechnologyAuthors: Suvisesha Muthu
Abstract: Metagenomics has revolutionized our understanding of microbial communities by enabling the study of genetic material recovered directly from environmental samples, bypassing the need to culture individual organisms. The explosive growth of metagenomic data has been driven by advances in high-throughput sequencing technologies, which present both unprecedented opportunities and considerable analytical challenges. Bioinformatics approaches have become indispensable in the processing, analysis, and interpretation of metagenomic datasets. This review provides a comprehensive overview of the main bioinformatics strategies and tools used in metagenomics, ranging from sequence quality control and assembly to taxonomic and functional annotation, comparative analyses, and visualization. The article discusses both the strengths and limitations of key methods and highlights recent developments that address scalability and accuracy in multi-omic integration. Special attention is given to computational frameworks enabling the discovery of novel diversity and metabolic functions in complex microbial communities, as well as the challenges posed by the massive volume and complexity of metagenomic data. Furthermore, we explore the growing emphasis on reproducibility, data sharing, and standardized pipelines in contemporary metagenomic research. By providing critical evaluation and synthesis of current bioinformatics methodologies, this review aims to serve researchers entering the field and experienced users seeking an updated perspective on state-of-the-art metagenomic analysis.
DOI: https://doi.org/10.5281/zenodo.16978173
