Analysis of Soil Metagenomes using the MEtaGenome ANalyzer (MEGAN)
Daniel H. Huson and Nico Weber
from: Omics in Soil Science (Edited by: Paolo Nannipieri, Giacomo Pietramellara and Giancarlo Renella). Caister Academic Press, U.K. (2014)
Soil is one of the most dense and diverse habitats of microorganisms, and metagenomics is a key technique for studying this environment. Given a dataset of DNA sequencing reads obtained from an environmental sample, the program MEGAN (Metagenome Analyzer) can be used to interactively perform an analysis and comparison of the data, both on a taxonomic and functional level. The program attempts to place all reads into the NCBI taxonomy and to map them to SEED functional roles or KEGG orthology groups. To compare various datasets, MEGAN allows the user to load multiple samples at once and combine them into a single comparison document. Multiple views makes it easy to inspect assignments to the different nodes. An alignment viewer is supplied to explore reference-guided multiple alignments of reads. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large datasets. It is written in Java and installers for the three major computer operating systems are available from https://www-ab.informatik.uni-tuebingen.de read more ...