Metagenomics involves the extraction, sequencing and analysis of combined genomic DNA from entire microbiome samples. It includes then DNA from many different organisms, with different taxonomic background. Reconstructing the genomes of microorganisms in the sampled communities is critical step in analyzing metagenomic data. To do that, we can use assembly and assemblers, i.e. computational programs that stich together the small fragments of sequenced DNA produced by sequencing instruments. Assembling seems intuitively similar to putting together a jigsaw puzzle. Essentially, it looks for reads “that work together” or more precisely, reads that overlap. Tasks like this are not straightforward, but rather complex because of the complexity of the genomics (specially the repeats), the missing pieces and the errors introduced during sequencing. In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing. Based on the 6 original dataset of the coffee fermentation system, we generated mock datasets for this tutorial.