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

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5.0 years ago

mrj ▴ 170

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 • 1.9k views

ADD COMMENT • link updated 2.3 years ago by Shawn • 0 • written 5.0 years ago by mrj ▴ 170

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

ADD REPLY • link 5.0 years ago by Bastien Hervé 5.3k

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Thank you so much. I will try this.

ADD REPLY • link 5.0 years ago by mrj ▴ 170

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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 2.3 years ago by Shawn • 0

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