Greengenes 341-805 classifier

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1

I have a greengenes 13_8 341-805 classifier I just trained with 2019.10 for anyone interested.

qiime tools import \
 --input-path gg_13_8_otus/rep_set/99_otus.fasta \
 --output-path ./gg_13_8_99_repset.qza \
 --type 'FeatureData[Sequence]'

qiime tools import \
 --input-path gg_13_8_otus/taxonomy/99_otu_taxonomy.txt \
 --output-path ./gg_13_8_99_taxa.qza \
 --type 'FeatureData[Taxonomy]' \
 --input-format HeaderlessTSVTaxonomyFormat

qiime feature-classifier extract-reads \
 --i-sequences ./gg_13_8_99_repset.qza \
 --p-f-primer CCTACGGGNGGCWGCAG \
 --p-r-primer GACTACHVGGGTATCTAATCC \
 --p-trunc-len 450 \
 --p-min-length 100 \
 --p-max-length 600 \
 --o-reads ./gg_13_8_99_341_805.qza

qiime feature-classifier fit-classifier-naive-bayes \
 --i-reference-reads ./gg_13_8_99_341_805.qza \
 --i-reference-taxonomy ./gg_13_8_99_taxa.qza \
 --o-classifier ./gg_13_8_341_805_classifer.qza
7 Likes
6

Got it! Thanks guys.
Btw Justine, there is a v3-v4 classifier for gg already in the community contributions, and there is a Silva one here too. Both trained with 2019.7 but should be compatible with 2019.10 too.

1 Like
7

I will check the threads, then! Thanks!

9

A post was split to a new topic: What is the principle behind naive baysian classification?

10

2 posts were split to a new topic: Finding the greengenes database

11

This is very interesting thank you for your support.

1 Like