Next-generation sequencing (NGS) platforms have revolutionized the study of the environmental microbiome, which comprises culturable and unculturable bacteria, archaea, eukaryotes, and viruses within a particular ecological niche. Amplicon and shotgun metagenomic sequencing approaches are now routinely employed to sequence the DNA of microbial communities in environmental samples. This article reviews bioinformatics tools used in the analysis of both short-read and long-read DNA sequence data. This rapidly growing field presents exciting research opportunities and challenges in software development, data and data analysis standards, data integration, and data interpretation.
