Example of a quantitative metagenomics pipeline. A metagenomics pipeline involves a series of sequential and crucial steps. Firstly, sampling of the relevant biological material and subsequent extraction of DNA are conducted in a standardized manner to ensure good-quality DNA in high nanogram or microgram quantity. Secondly, a library is prepared by fusing DNA fragments with adapter molecules followed by PCR amplification and next-generation sequencing, which produces millions of short reads (about 150 to 800 bp depending on the sequencing platform) that are then assembled into longer contigs. Finally, microbial genes are identified and annotated to known functions or taxonomic units based on homology searches against available reference catalogs. For further details see .