How do I extract out ITS region from assembled whole genome sequence of a fungi?

3

Entering edit mode

5.6 years ago

mrj ▴ 180

Hi, I am trying to make a computational identification of a whole genome fungal sequence. At the moment, I have a fungal whole genome sequence (300 contigs - fasta sequences). I am thinking of extracting out only the full ITS region. I am wondering what tool I can use to do this and an acceptable protocol to follow.

Thank you

genome Assembly alignment • 2.2k views

ADD COMMENT • link updated 2.9 years ago by Shawn • 0 • written 5.6 years ago by mrj ▴ 180

2

Entering edit mode

Found this but never used : https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12073

ADD REPLY • link 5.6 years ago by Bastien Hervé 5.9k

1

Entering edit mode

Thank you so much. I will try this.

ADD REPLY • link 5.6 years ago by mrj ▴ 180

0

Entering edit mode

Did you ever find a solution to extracting the ITS region from the full genome sequence? I am currently working on a similar project now. Thank you for any help or advice!

ADD REPLY • link 2.9 years ago by Shawn • 0

Login before adding your answer.