DIAMOND + MEGAN Microbiome Analysis

• DOI: 10.1007/978-1-0716-3072-3_6
• Publication Date: 2023-05-31T21:02:43Z
• Authors: Anupam Gautam; Wenhuan Zeng; Daniel H. Huson
• Keywords: Databases, Factual; Microbiota; Metagenome; Sequence Analysis, DNA; Metagenomics; Software; Algorithms; 004

Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.