Workflow data files for core pathogens

As part of our Nextstrain-maintained analyses we generate workflow files such as sequence FASTAs and metadata TSVs. This page lists the latest versions of these files as well as providing a window into the history of the file uploads across time. The available Auspice visualisations related to these workflow files are shown at the /pathogens page.

Each filename below is a clickable (external) link which will download the latest version of the particular file. Hovering on a filename shows the last known update date however our knowledge of this lags by a day or two and so a more recent copy may be available; if this is the case the link will point to the latest version.

The 'show full history' link details the temporal history of files for a given pathogen.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions.

Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

Some of these files contain Restricted Data from Pathoplexus.
To use these in your own analysis, please read Pathoplexus Restricted Data Terms of Use.