Overview
Overview
About
General informations about features, how to cite, demo projects, funding and additional links.
Install MGX
Needed prerequisites, Java JDK Version 17, Supported operating systems and obtaining MGX.
Basics
Obtaining a Project, MGX Roles, metadata, Connect to a server, uploading own files, importing reference genomes and search.
Projects
Handling a Project by creating a new habitat, creating new samples and DNA extracts and how to import sequence data
Analysis
How to perform quality control, select a analysis pipeline and monitor the selected jobs.
Assembly
How to assemble a metagenome or metatranscriptome.
Visualization
How to visualize the results, export sequences, get biodiversity indices and display reference mappings.
Custom Pipelines
Create custom analysis pipelines within MGX.
References
Altschul et al., 1990 Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990).Basic local alignment search tool. Journal of molecular biology, 215(3):403–410. Hughes et al., 2002 Hughes, J. B., Hellmann, J. J., Ricketts, T. H., and Bohannan, B. J. (2002). Counting the uncountable: Statistical approaches to estimating microbial diversity. Applied and environmental microbiology, 68(1):448. Langmead and Salzberg, 2012 Langmead, B. and Salzberg, S. L.
