Metagenomics: Focusing on the Haystack

Abstract

Metagenomics enables the genomics study of uncultured microorganisms, using inexpensive sequencing methods. This chapter provides a concise but comprehensive overview of the current computational methods in metagenomics and the recent progress made. The strategies, methods, software, and protocols generally used for metagenomics analysis of all environmental communities are discussed. Moreover, the challenges in the field of metagenomics, including applications where metagenomics analysis has opened up ways of investigating symbiosis, metabolic pathway construction in metagenomes, gene family enrichments, and disease association studies, are discussed.