Beta Version 0.3.8

We are excited to release version v0.3.8 of Apollo 3, which includes many new features inspired by feedback from users. Below are some of the changes since v0.3.6 that we'd like to highlight.

Also, when updating Apollo 3 to this version, please make sure to also update JBrowse 2 to at least v3.6.5 as there are some important stability improvements that require JBrowse 2 to be updated to take effect.

New features

Apollo Reference Sequence Track

Prior to this release, Apollo would draw the sequence directly on the "Annotations" track if you were zoomed in close enough. However, this could cause the annotations to jump around depending on the zoom level, and there was no way to hide the sequence for users who didn't want to see it.

In this release, instead of being drawn directly in the "Annotations" track, the sequence is available as the default display in the built-in "Reference sequence" track, allowing it to have its own dedicated space. The interactions with the "Annotations" track, such as highlighting the currently hovered CDS, still work the same, and if needed the default JBrowse sequence display can be toggled on from the track menu.

Merge and split exons

There is a new command that will merge two exons into a single one, as well as an accompanying command to split an exon into two separate exons.

Merge transcripts

Transcripts can now be merged, and Apollo 3 will create a new transcript with its subfeatures automatically calculated from the overlap of the source transcripts.

Redo

In addition to the existing "Undo" functionality, "Redo" is also now available from the top-level Apollo menu.

Go to neighboring exons

A new method of navigation is available in the form of the menu items "Go to upstream/downstream exon". This is especially useful when navigating at a high zoom level in genes with large introns.

Locked mode

A new option is available from the top-level Apollo menu that allows you to lock and unlock editing. When locked, no edits are able to be made, allowing you to be able to freely explore the data without risk of accidental editing.

Improved functionality

Labels in six-frame view

The six-frame view now provides labels for its features. These can also be disabled in the track menu for a more compact view.

Filter transcripts in six-frame view

In the six-frame view, if there are alternate transcripts and you want to focus on just one of them, you can now select which transcripts to filter out of the current view.

Copy feature from alignments track into an existing gene

Read features in a JBrowse alignments track (such as from a BAM or CRAM file) can now be copied as transcript features into an existing gene, in addition to the being able to create a new gene.

Right-click menu lists all features for a location

The right-click (a.k.a. context) menu for gene glyphs has been updated to show actions for any features that overlap the current location.

Check results clustering

Check result warning symbols are now clustered together when they overlap, which helps prevent clutter in the display. The warning symbols can also be turned off completely from the track menu.

Background colors for noncoding transcripts

Features with the type "pseudogene" or transcripts with the type "pseudogenic_transcript" are now rendered with a blue background so they can be easily visually identified. Similarly, any other transcripts that do not have a CDS (such as those of type "lncRNA") are rendered with a red background.

Selection of added features

When you add a new feature, whether top-level or a child feature (i.e. a transcript), the feature is now selected in the UI allowing you to more easily identify it.

For more information

For more details on any of the changes mentioned as well as many more changes that have been made, please reference the associated GitHub issues.

• Improve click and drag actions by @garrettjstevens in #595
• Improve transcript widget edit location action by @shashankbrgowda in #598
• Feature expand/contract rows for feature labels in LinearApolloSixFrameDisplay by @haessar in #579
• Show details widget when we click on feature in gene glyph by @shashankbrgowda in #576
• Show feature details widget on click when in LASFD by @haessar in #602
• Add ability to merge and split exons by @dariober in #574
• Show all genes in the region as destination when adding feature from evidence track by @shashankbrgowda in #588
• Alternate transcripts filtering for LinearApolloSixFrameDisplay by @haessar in #591
• Update Cypress tests to work on latest JBrowse by @garrettjstevens in #614
• Fix and improve adding feature from BAM track to Apollo track by @shashankbrgowda in #607
• Make context menu list all possible features for that location by @dariober in #618
• Add open transcript details option on right click of child feature by @shashankbrgowda in #608
• Print gff_id when reporting errors by @dariober in #610
• New gene or transcript must have strand set by @dariober in #619
• Fix loading non-Apollo plugins from stored config by @garrettjstevens in #613
• Split docker build action by platform arch by @amorison in #616
• Add "Merge transcripts" action by @dariober in #604
• Add option in UI to download GFF without FASTA by @dariober in #625
• Add ability to configure assembly aliases in the UI by @shashankbrgowda in #620
• Fix undo only undoing the last change by @dariober in #622
• Improve click and drag actions in LASFD by @haessar in #624
• Fix:Update CDS locations for translation trim without validation by @shashankbrgowda in #609
• Fix copy to clipboard not working in some contexts by @garrettjstevens in #627
• Resize gene/transcript after deleting exon by @dariober in #632
• Fix reverse strand protein translation in sequence panel by @garrettjstevens in #628
• Update test image snapshots by @garrettjstevens in #648
• Context menu list for LASFD by @haessar in #644
• Make the "hovered feature" available to all displays on the session by @garrettjstevens in #641
• Add custom display to reference sequence track, don't render sequence on Apollo track by @garrettjstevens in #642
• Fix LASFD tooltip rendering bug by @haessar in #651
• Fix file path retrieval in desktop by @garrettjstevens in #652
• Bring LASFD into line with recent changes to reference sequence track by @haessar in #655
• Add justfile and instructions for developers by @amorison in #638
• Add more custom component extension points to the transcript widget by @garrettjstevens in #649
• Redo functionality - issue #629 by @dariober in #645
• Add menu item to hide/show check results by @haessar in #653
• Keep all attributes of merged features by @dariober in #640
• Add sequence length to and reformat the sequence ...

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