Beta Version 0.3.6

We would like to thank all those who have given feedback on Apollo 3 since our initial beta release of version v0.3.0 in December. We have continued to work on improving the experience for Apollo 3 users over the course of several versions, and we'd like to highlight some of the new features we've completed between then and our newest current release, version v0.3.6.

New features

Add feature from JBrowse 2 gene track

Right-click on a feature such as a gene in a JBrowse 2 evidence track and select "Create Apollo annotation" to create a new Apollo annotation from that feature. Attributes on the feature are also copied into the new Apollo annotation.

Filter visible features in the display

From the track menu, select "Filter features by type" to filter what features are available in the Apollo track. This could be used, for example, when you want to focus on a subset of all your annotations, such as pseudogenes.

Export GFF3 using Apollo CLI

Previously GFF3 export was only available from the Apollo menu in the UI. Now it can also be done with the Apollo CLI.

apollo export gff3 myAssembly > out.gff3

Protein sequence now included in transcript details

The "Sequence" section of a transcript's details widget now includes the option to view the protein sequence.

Tip

For any of the sequence viewing options, the sequence is in FASTA format. When you use the "Copy sequence" button, the FASTA sequence can be pasted in plain text format (e.g. in a text editor) or with the color highlights (e.g. in Google Docs).

Improved transcript details widget

The transcript details widget now includes a more compact summary of the transcript. It also includes the transcript's protein translation with start and stop codons highlighted as well as the ability to "trim" the CDS to match the nearest start and stop codons if needed with a single click.

More options available in "Add new assembly" in the UI

The "Add new assembly" dialog in the UI has been improved to add functionality that was previously only available in the Apollo CLI.

Shortcuts in "Add a feature"

When adding a new feature from scratch, there is now a shortcut to add a gene or transcript with all the necessary subfeatures in a single action.

Tip

Access the "Add a feature" dialog by selecting an area in the view ruler track and choosing "Add new feature" from the menu.

Six frame display

A new display type, the Apollo Six-frame Display, is available for Apollo tracks. It can be accessed from the track menu under "Display types."

This type of view is inspired by the Artemis genome annotation tool and will continue to be updated with more functionality.

Improved functionality

Sequence ontology used to compare equivalent terms

Improvements have been made in using the the configured feature ontology (by default the Sequence Ontology) to detect valid terms for various annotation structures. Any valid ontology terms can be used. For example, you could use the term "exon_of_single_exon_gene" instead of "exon" and Apollo will automatically recognize that as a valid term for the child of a transcript without any additional configuration.

Non-coding genes now render with a gene glyph

Genes without a coding sequence, such as pseudogenes or ncRNA genes, now have improved rendering to match that of coding genes.

Upcoming

Customization

We are working on expanding the options to customize Apollo to fit your own
needs. Stay tuned for more information on this soon.

Apollo 3 Genome Annotation Editor - Beta Release

Thank you to all those who have shown an interest in Apollo 3, our tool for collaborative genome annotation.Due to Apollo 3’s flexible client-server architecture, there are a few different ways you can use it, both single-user to collaborative, and using demo servers or configuring your own data. We would like to introduce four different ways you can try out Apollo, ranging from taking a quick look to provisioning a full multi-user installation.

How to try it out

1. Quick-look demo

To quickly see what Apollo looks like and get a basic idea of its functionality, visit this link:

Try Apollo now!

Log in either as a guest or use a Google account.

The genome annotation database you see when you open this link represents a small slice of a genome stored directly in your JBrowse session. This genome database is not collaborative: anything you change is limited to your current browsing session and is only visible to you. Anything you do on this genome won't affect anyone else's experience, so feel free to experiment however you like. If you want to start fresh again without any of your changes, you can open the original link again.

2. Full demo

If you want to explore some larger genome annotation databases that are collaborative (meaning any changes you make will be visible to other users), there are a few other genomes loaded on our demo server.

Click the link given in the quick-look demo above, go to the "Add" menu and choose "Linear genome view," choose either "Schistosoma haematobium" or "Schistosoma mansoni," and click "Open". To see the Apollo track, open the track selector and choose the "Annotations" track.

3. Running Apollo on your own computer

If you'd like to try setting up Apollo yourself, either with data we provide or with your own data, this tutorial on our website walks you through setting up an Apollo instance that runs on your own computer, with all the steps for configuring the server and loading data. This is a great way to test Apollo out before doing a full multi-user installation

4. Deploy a multi-user Apollo instance to a server

Our
deployment guide walks you through installing a fully-featured multi-user Apollo instance on a server, allowing you to take advantage of Apollo's collaborative features to annotate your own genomes.

What's next?

We have a lot of plans for user interface improvements to make annotating easier. The official Apollo website is apollo.jbrowse.org, where you can find all the docs and announcements, including periodic new features and releases.

We welcome questions in our discussion forum and bug reports on GitHub.

Best wishes, The Apollo Team