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Metagenomics is defined as the study of the metagenome, which is total genomic DNA from environmental samples. Metagenomics has long been one of the major research tools in microbial ecology since the term was first used in 1998 (Handelsman et al., 1998). Metagenomics has become an indispensable tool for studying the diversity and metabolic potential of environmental microbes, whose bulk is as yet non-cultivable. Due to the differences between the metagenomic data obtained from whole genome sequencing and amplicon sequencing methods, there are significant differences between the corresponding bioinformatics tools for these data.