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Beta Version 0.3.8

· 7 min read
Garrett Stevens
Apollo Developer

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.

Apollo sequence track

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 and split exon feature menu items

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.

Merge transcript feature menu item

Redo

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

Redo top level menu item

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.

Go to neighboring exon feature menu items

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.

Six frame view row labels

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.

Six frame view transcript filter

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.

Copy alignments read to existing 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.

Context menu for multiple features

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.

Clustered check results

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.

Feature type backgrounds

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.

New Contributors

Full Changelog: https://github.com/GMOD/Apollo3/compare/v0.3.6...v0.3.8