how to generate a unigene set

[Kennels]

Hi,

I see alot of transcriptome assembly papers discussing a de novo assembly, and then generating 'unigenes' from the redundant contigs, for some definition of unigene.

How does one usually go about generating a unigene set from the raw contig assembly set. Any particular software that does this?
e.g. I was looking into this and some seem to use cd-hit-est program?

thanks,

[SES]

There are many ways to approach this, but one straightforward approach would be to use usearch. Take a look at the manual as there is a specific section with exact commands for generating non-redundant databases.

EDIT: I've had problems with usearch using too much memory (for a typical desktop machine) so I wanted to throw in another option. You may want to also consider trying Vmatch. Section 9.9.8 (page 60) of the Vmatch manual shows you the commands for creating a non-redundant set of sequences.