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Microbes are involved in plenteous activities, where numerous groups are responsible for positive events, such as environment purification, industrial applications, and medicinal applications, and a few causes negative health issues. Their remarkable activities demand thorough analysis comprising accurate knowledge about taxonomic and functional hierarchy. Metagenomics, a fast-growing research field, deals about uncultivated microbes to evaluate their true diversity and functions using various computational and biological technologies for analysis and information extraction from environmental samples. Nuclear components’ sequencing is a fundamental requisite for metagenomics study. Currently, sequenced metagenomes exceed several millions while rapidly growing with advanced high-throughput sequencing technologies. Comparison of multiple datasets is obligatory for metagenomics analysis but always remains challenging. Experimental conditions, sequencing errors, genomic duplications, and cumbersome downstream analysis can highly influence data interpretations. Therefore continuous need exists for faster and user-friendly advanced methods to overcome these challenges. This chapter describes advanced metagenomics approaches, tools, possible challenges and addressing the issues considering a dataset from mangrove soils as case study. |
