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I haven't looked into it because I'm sequencing ITS2. You can use mothur rather than qiime-more flexible you can use any reference database you'd like -
mycofier - new tool for ITS - anyone got it working yet?
Having trouble getting this to work. Any one else using this program yet? It would be nice to ahve an alternative to Qiime / uparse and Unite db.
cheers,
S.
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