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add taxonomy classification method #5

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nbokulich opened this issue Jan 2, 2017 · 2 comments
Closed

add taxonomy classification method #5

nbokulich opened this issue Jan 2, 2017 · 2 comments

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@nbokulich
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It could be useful to add a taxonomy classifier to the vsearch plugin, mirroring the functionality of the qiime1 uclust classifier.

An example command that I had used previously for this, showing (at least the basic) parameters needed:
vsearch --usearch_global <input fasta> --db <ref seqs> --uc <output file> --id <% similarity> --strand both --maxaccepts <int> --maxrejects <int> --uc_allhits --output_no_hits

This outputs .uc files, so a conversion method akin to taxter's uc_consensus_assignments may be needed.

@gregcaporaso
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gregcaporaso commented Sep 25, 2017

@nbokulich, do you think this is still something that should go in q2-vsearch, or would it make more sense in q2-feature-classifier? I think the latter, so I'm going to close this, but let me know if you disagree and we can discuss.

@nbokulich
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already in q2-feature-classifier — sorry, I should have circled back to close this issue when I added that method.

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