Persephone can connect to external data sources and simplify the process of importing their data. To open the Connect external data sources dialog, click on the Connect button in the bottom-right corner of the Map Set tree:

Every tab at the top of this dialog represents an external database. At present, you can browse and import data from NCBI Datasets as well as Track Hubs.

NCBI Datasets

To open an NCBI assembly, type a search term in the search box and press Enter (or click the Search button). You can search for an exact NCBI accession (GENBANK or REFSEQ); or for an organism by its common or taxonomic name:

By default, the list of available assemblies displays assembly name, organism, accession, and the number of available chromosomes and contigs for each assembly. As always, you can edit the list of columns if you wish to see more data, e.g. Total sequence length:

You can also quick-search, filter, or sort the list of assemblies by their column values; for example, you could choose to show only REFSEQ assemblies:

Click an assembly to open it:

NCBI Assembly details

This view opens to display all tracks in the NCBI assembly that are available for import. You can also click the Sequences tab at the top to view the available genomic sequences, or click the Dataset Report tab to view the raw assembly metadata from NCBI. The links in the upper-right corner of the dialog will open in new browser tabs to show the original NCBI sources for this assembly:

• NCBI FTP repository: Opens the FTP repository where all of the source files are stored; note that this repository may contain additional data files (notably variants in VCF format) that cannot yet be imported automatically. You may still be able to copy the URL to one of these files, then import them manually using Persephone's standard Import dialog.
• Open in NCBI Datasets: Links directly to NCBI's web page for the currently selected assembly, listing its metadata, statistics, associated publications, and other useful information.

In addition, you can right-click any track and select the Copy file URL option to copy a direct link to its source file to the clipboard:

If you wish to select a different assembly, click the Back button in the upper-left corner to go back to the assembly search results.

The  Import mode selector determines where and how the imported data will be stored.

Import mode: Quick View

This mode is only available for NCBI data sources (and is the default). It is designed to provide quick and robust access to NCBI's data, and is the best option if you wish to quickly browse the assembly without performing in-depth analysis. When Quick View is selected, a checkbox appears next to each track; check the box to select the track for import. The associated genomic maps will be automatically selected for import into a new Map Set:

Once you are done making your selections, click the Add button on the bottom-right. Persephone will then begin loading the selected tracks to shared storage. If you or any other user had previously requested these tracks, they will be available instantly; otherwise, the import process may take some time. You can check on its progress by clicking the notification icon on Persephone's main toolbar:

Once the tracks have been loaded, Persephone will automatically display the first available map (typically Chromosome 1). The checkboxes next to each imported track will change to icons; click one of these icons to remove the associated track from Persephone (you can always bring it back by checking its checkbox and clicking Update). The assembly (and all of its tracks) resides in its own Map Set, organized under the teal-colored Quick View node in the Map Set tree:

Thus you can always browse the NCBI assembly's maps by selecting its Map Set in the tree. In addition, its associated Map Set will be indicated in the assembly list, as well as in the Assembly details view:
       

Click the Map Set's label to open its details, or click the icon to navigate to the imported Map Set in the Map Set tree. 

In addition, the Assembly details view is automatically displayed in the Map Details and  Map Set details dialogs, in a separate tab at the top:

The Quick View mode supports most of the core functionality in Persephone; for example, you can view Annotation details for gene annotations (along with their transcripts and sequences), drill down into BAM read details, produce instant Sequence alignments using BLASTN and minimap2, and so on. However, some functionality is not yet available in Quick View mode. For example, you cannot attach your own tracks to Quick View Map Sets (other than the tracks available at NCBI); nor can you run BLAST against them in bulk nor search for track features by name. 

To apply the full range of Persephone's features to the external tracks, you must change the Import Mode selector to one of the other two options: Private Storage or Local Session. Both of these options are shortcuts for Persephone's general Import workflow.

Import Mode: Private Storage

In this mode, imported files will be loaded into your long-term private storage, and attached to one of the previously loaded Map Sets, either in Persephone's main database or in your own private storage. 

In many cases, you would first want to import the genomic sequences into a new Map Set. To do so, click the button next to the prospective Map Set (always shown at the top of the list):

Persephone will then open its standard Import dialog, and begin loading the sequences:

On the next screen, you can choose which maps should be imported and which should be discarded, edit their map names and chromosome names, and so on; or you can just click Next to accept the defaults and import all available maps. The screen after that allows you to change the new Map Set's organism and visible name, as well as its description.
       

Finally, the newly imported sequences will be indexed for BLAST, and the new Map Set will appear in the Map Set tree. It will also be automatically selected in the Map Set selector:

You can now begin loading additional tracks in this NCBI assembly, and attaching them to the newly loaded Map Set. Alternatively, you can click the dropdown button to select another Map Set:

To load a track, click the button next to it. For example, you can choose to import the gene annotation track; Persephone will then begin loading the source file:
       

On the next screen, you will be prompted to assign maps in the source file to the previously loaded sequences in the Map Set. In this example, both the gene annotation track and the sequences came from the same NCBI assembly, and so their map accessions should match perfectly; check the Use Map Accession checkbox to perform the match:
       

Alternatively, you can perform the match manually, choosing which maps to import and which to skip, and you can even select a different Map Set if desired. Note that, while NCBI assemblies are manually curated and generally accurate, some of the data files may still contain mistakes. For example, in this case one of the contigs contains annotations that lie outside of its genomic sequence:

A small number of such warnings (indicated by icons in the map list) is usually acceptable; but if most of the maps display warnings, then you should double-check the currently selected Map Set to make sure that it refers to the correct version of the genome. 

On the next screen, you will have the opportunity to change the properties of the newly imported track (such as its name and color). Finally, the track will be indexed for BLAST and text Search, and the newly loaded track will appear on the map:

The track will be shown with a teal background, indicating that it is stored in your long-term private storage.

Loading tracks into long-term private storage is the most robust option, but doing so takes additional time and consumes your storage quota (also, some data formats cannot be loaded into private storage at this time). The alternative is to load tracks into your local browser session.

Import Mode: Local Session

In this mode, tracks are loaded into your local browser session directly from the remote data source (e.g. NCBI or a Track Hub). Tracks loaded in this manner will disappear when you close the browser (or reload Persephone's browser tab); however, they can be displayed almost instantly and consume no storage quota. This mode is especially useful for large data files such as BigWig and BAM tracks.

To display a track in the local browser session, click he button next to it. Note that some of these buttons may be disabled, usually because the source file's data format is not yet supported for local session viewing:

Fortunately, BAM files are supported. To view one, firs select a Map Set with the corresponding genomic sequences as described above (you may first need to import the sequences as a new Map Set in your private storage). Once you click the button, Persephone will display an abbreviated map matching form, prompting you to assign maps in the input file to maps in the selected Map Set. As before, matching by map accession will most likely prove sufficient:

Note that in this example the input file contains data for only some of the maps in the underlying assembly, not all of them -- such cases are not uncommon. When you finish map matching, click Done, and the imported track will appear on the map:

The track will be shown with a pink background, indicating that it is loaded into the current browser session, and will disappear when you close Persephone.

Track Hubs

(coming soon)