Bioinformatics pipelines for Metagenomics: A review of data processing and functional annotation approaches

Abstract

The diverse environment from soil and air to marine ecosystems and the human gut and hidden places on the earth is a treasure island of metagenomes of microbial consortia. Metagenomics, with the capability of culture-independent characterization of microbial communities can help in understanding the complexity of microbial populations. This work presents a novel, integrative framework that connects strategic omics and sequencing technologies to combine sophisticated metagenomics studies with customized next-generation sequencing techniques. The widespread applications of bioinformatics tools for diverse metagenomic approaches have created a fragmented methodological domain, making tool selection and pipeline design challenging for researchers. This review focuses on current sequence processing and functional annotation approaches in metagenomics, comparing tool performance, computational software requirements and their implementation and application.   This study explains a hybrid sequencing method that enables the recovery of whole biosynthetic gene clusters and improved assembly of low-abundance microbial genomes by merging long-read nanopore data and short-read Illumina platforms. In addition to improving traditional metagenomics methodologies, the integrative approaches covered in this review result in a scalable, repeatable procedure that can be used with a variety of microbiome types. This review explains how strategic analysis techniques can uncover hidden functions, uncommon taxa, and microbe-microbe interactions that are frequently overlooked in conventional studies. The novelty of this review lies in laying the groundwork for next-generation ecological predictions and precise microbiome engineering with proper data analysis protocols.