Does it necessary to have an assembled genome to run PiRATE pipeline about pirate HOT 2 CLOSED

Dear Majie,

Thanks for your message and interest about PiRATE.

PiRATE is very flexible, you can only use the tools that are interesting for your study. It's a kind of platform with a of lot of tools to help you to achieve what you want.

Thus, you don't need to have a genome assembly to use some tools.

For exemple if you want to know what types of TEs are in the genome of the species you are studying, you can only use the tools of the approches 4 (detection step), and then use PASTEC (classification step). You will got a library of TEs that are in the genome.

But, because you do not have a genome assembly you will not use TEannot (annotation step).

Hope this will help you,

(no problem for the duplicate)

Best regards,

Jeremy

from pirate.

Hi @JBerthelier ,
Got it, Many Thanks.

from pirate.