Dear Ranjeet, Currently I am working on annotation part of de novo assembled genome. I am using MAKER pipeline. It provides multiple tools to generate complete annotation (almost) and output in different formats starting from GFF3 and also has many supporting scripts such as converting MAKER output to Jbrowse compatible tracks. Here is the link for MAKER tutorial "http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014"

commented on this link "C: Annocript: completely automated transcriptome annotation pipeline which can also"

Hello Ranjeet,

If you have short-read RNA-Seq samples, you could try our new genome annotator finder. It uses short reads to construct gene and transcript structures and additionally uses protein data but can also work without it. finder also runs BRAKER2 inside to enrich the gene repertoire with predicted information. You can access the paper from FINDER and the software is in Github

Thank you.