transcript annotation software

Question

[Ric]

Hi, Is there better annotation software than trinotate?

[h.mon]

What are the shortcomings you perceive on Trinotate? What you wish was better?

My one gripe with Trinotate is it is tailored for Trinity, and do not integrate well with other transcriptome assemblers. As I mostly use Trinity for assembly, this is not an issue for me.

Alternatives (among others):

https://github.com/frankMusacchia/Annocript

https://github.com/camillescott/dammit

[Ric]

Trinotate does not provide any gff3 or gtf as final output. Or does anyone has script how to create to convert to gff3 or gtf?

Answer 1

[GouthamAtla]

I cant say better or not, but you could check Annocript