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Add q2-feature-classifier as an option #9

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cjfields opened this issue Aug 19, 2020 · 1 comment
Open

Add q2-feature-classifier as an option #9

cjfields opened this issue Aug 19, 2020 · 1 comment
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DSL2 Prioritize for DSL2 implementation enhancement New feature or request

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@cjfields
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This seems to work pretty well with PacBio and Loop full length 16S runs and the full-length trained data. On our local cluster using the QIIME2 output from the pipeline:

module load QIIME2/2020.6
qiime feature-classifier classify-sklearn --i-classifier QIIME2/silva-138-99-nb-classifier.qza --i-reads sequences.qza --o-classification tax_final.qiime2.qza --p-n-jobs $SLURM_NPROCS
qiime tools export --input-path tax_final.qiime2.qza --output-path tax_final.qiime2
@cjfields
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Note that a dada2 Silva database is also now available for this step, which works well with internal data (both Loop and PacBio).

@cjfields cjfields added the enhancement New feature or request label Nov 30, 2021
@cjfields cjfields added the DSL2 Prioritize for DSL2 implementation label Aug 23, 2024
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Labels
DSL2 Prioritize for DSL2 implementation enhancement New feature or request
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