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
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.
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!