Need to compile metadata to perform trait associations using our metagenomic data? Interested in correlating species abundance with the origin of the sample to identify organisms associated with a particular environment or state? Try our latest metagenomics toolkit (called: “mg-toolkit”) - a beta version of a tool to enable scientists to download all of the sample metadata for a given study to a single csv file. Simply install as follows:

$ pip install -u -U mg-toolkit
$ mg-toolkit original_metadata -a ERP001736 

or use it directly from within your Python script:

>>> from mg_toolkit.metadata import OriginalMetadata
>>> om = OriginalMetadata("SRP034967")
>>> om.save_to_csv(om.fetch_metadata(), "SRP034967_metadata.csv")

We will add more useful tools to help processing metadata and annotations in the future.

Metadata matters!