import fungi classifier for ITS region

Dear all,

I would like to analyze fungi community from my samples. We have amplified samples using ITS1F and ITS4 primers. I have download classifiers from UNITE /PlutoF DOI). In the compressed file you can find two types of files (.fasta file with all the sequences and a .txt file with the classification). How can I import this classifier? Should I import only the fasta file or both files? I am aware that in the .txt file I cand find the classification and so it is important also to include this information in the resulting .qza taxonomic classifier.

  • Files from the classifier:
    sh_refs_qiime_ver9_dynamic_29.11.2022.fasta
    sh_taxonomy_qiime_ver9_dynamic_29.11.2022.txt

qiime tools import
--type 'FeatureData[Sequence]'
--input-path sh_refs_qiime_ver9_dynamic_29.11.2022.fasta
--output-path sh_refs_qiime_ver9_dynamic_29.11.2022.qza

qiime tools import
--type 'FeatureData[Taxonomy]'
--input-path sh_taxonomy_qiime_ver9_dynamic_29.11.2022.txt
--input-format TSVTaxonomyFormat
--output-path sh_taxonomy_qiime_ver9_dynamic_29.11.2022.qza

Which one should I import to obtain the .qza of the taxonomic classifier?

Thank you very much for your help

Best regards

Bea

Hi Bea!
To my understanding, what you have downloaded is the parts needed to train a classifier, not a ready-to-go classifier.

To get the classifier, you could do the following:
qiime feature-classifier fit-classifier-naive-bayes
--i-reference-reads sh_refs_qiime_ver9_dynamic_29.11.2022.qza
--i-reference-taxonomy sh_taxonomy_qiime_ver9_dynamic_29.11.2022.qza
--o-classifier fungal-classifier.qza

That should get you your classifier, which you can then use with qiime feature-classifier classify-sklearn.

This page may be of good help: feature-classifier — QIIME 2 2023.5.1 documentation

1 Like

Thank you so much for your quick answer!

This is exactly what I did after posting this message and looking for more information in qiime forum.

As you said, I thought that one of these files were the ready-to-use classifier.

Thank you

Bea

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