De novo bacteria transcriptome assembly options

Question

[hac141]

Hello, I am relatively new to transcriptome analysis, definitively new to de novo assembly. I wonder if anyone knows of a good option to assemble a bacterial transcriptome in the absence of a good reference genome? So far I have not been able to find a publication on this topic.

Thanks!

Answer 1

[st.ph.n]

You can use Trinity for de novo transcriptome assembly.

Answer 2

[Asaf]

It's relatively easy (compared to eukaryotes). You can use software for DNA assembly but make sure it doesn't assume even coverage. rnaSPAdes or metaSPAdes should work.