Best genome browser for manual curation of gene structure(s)?

Question

[William]

What is currently the best genome browser for manual curation of gene structure(s)?

The genome browser should at least be able to:

• load a reference gene model (i.e. a GTF/GFF3)
• load short read and long read RNAseq tracks (i.e. BAM/CRAM files)
• via drag and drop of the RNAseq reads, create or modify gene structure. Store the created/modified gene structures in some backend.
• export the curated genes as a new GTF/GFF3 file

Answer 1

[cmdcolin]

Apollo 2 (https://genomearchitect.readthedocs.io/en/latest/) may fit the bill for manual gene annotations. It is unfortunately somewhat tricky to setup, and has not been maintained very much over the years. There really should be a TL;DR on the Apollo docs, you can basically clone the repo, then run "./apollo run-local" and it will launch a in-memory h2 database (and there are setups for persisted mysql and postgres too). let me know if you need any help setting up

Another tool that i stumbled across for manually editing gene annotations is called GSAMan. I think is not very commonly used but has some impressive demos, it's a IGV extension. link here https://www.yuque.com/cjchen/ra7ghy/udlbcgx4ygcb4l0k first saw here https://twitter.com/c_jchen/ status/1682550280045359104

disclaimer: I was involved in Apollo 2 development

[William]

Thank you for the information. Is Apollo2 still the main used version of Apollo? I see there also is a (development) version of Apollo3, but I am not sure what the status of Apollo3 is. Anyhow it is somewhat strange that there are not more tools for curating gene structure, given there are many species and automated gene structure prediction can't solve the full task. So thank you also for the work that went into Apollo2.

[cmdcolin]

Yep, I'd say Apollo 2 is the best bet for now. Apollo 3 is under development and aiming for a release later this year from what I know. I definitely agree that these tools are very important!