- Course overview
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- What is MGnify?
- MGnify data
- Study overview
- Sample overview
- Analysis pages
- Sequence search
- MGnify genomes
- Requesting assembly and/or analysis by MGnify
- Submitting data to MGnify
- Your feedback
- Get help and support on MGnify
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MGnify data
MGnify data structure
Data in MGnify is structured into projects, samples, runs and analyses. Each project contains one or more samples, and each sample can have one or more experiments associated with it (such as metagenomic, amplicon or metatranscriptomic). Analyses are the results obtained from processing a run file (or an assembly derived from the run file) using a given version of the pipeline.
Samples and runs are indexed using ENA assigned accessions. MGnify studies and analyses have their own identifiers of fixed length composed of a common prefix (‘MGY’), a letter corresponding to the data type (‘S’ for study, ‘A’ for analysis) and a unique eight-digit number. ENA study accessions are also recognized in the different search tools available on the website.
Projects, samples and runs can be accessed by navigation using the various search and browse functions available on the front page.
Basic data searching in MGnify
MGnify can be searched using the text box on the front page, or via the ‘Text search’ tab. The results can be filtered to narrow down the information shown. For example, searching with a word or phrase (e.g. ‘Gut’) will show only those projects or samples with metadata containing that term. The data can be further explored using the facets provided (Figure 2A), including biome, experiment type, and sequencing platform. It is also possible to search for analyses that contain a certain type of organism or that encode proteins capable of particular functions (in the form of InterPro annotations of GO terms). A fully featured API is also provided, allowing users to build more complex queries and download the corresponding output.
Data can also be accessed using the ‘Browse data’ tab. Within this page there are further tabs for ‘Super Studies’, ‘Studies’, ‘Samples’, and ‘Publications’. Keyword filtering is available for all options, and in the case of studies and samples, it is also possible to filter for your biome of interest (Figure 2B).
However you choose to navigate to your study of interest, clicking on the MGnify accession (of format MGYS) will take you to the study overview page for that study.