ITS database other than UNITE database

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1

Hi,
I have utilized UNITE for my ITS analysis. Now, I am interested in testing another database. Does anyone know of an alternative pre-fitted sklearn-based taxonomy classifier ? I came across a related question on this forum (ITS database other than UNITE), but the provided links appear to be inaccessible.

Any suggestions for alternative ITS databases would be greatly appreciated.

2

Hi @Scalett_Pegany,

As far as I know RDP is no longer maintained. Hence the website is no longer available. However, you can download the RDP files from SourceForge here. It looks like the fungal ITS warcup is quite old (2016). Perhaps someone else has more information.

You can also make use of RESCRIPt, to make your own databases. For example:

-Mike

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@SoilRotifer Thank you for your response. I am currently using qiime2-2022.8.3. Could you please guide me on which file I should download from this website: RDP Classifier - Browse /RDP_Classifier_TrainingData at SourceForge.net? (could you provide the name of the required file?)

I appreciate any assistance.
I also hope that someone else may have more information on this matter.

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If you look at the file names you'll see that there is one labeled fungalits_warcup_trainingdata1.zip. I think that should be the one.

1) Unzip the file.

2) Parse Taxonomy from the fasta file:

egrep '^>' Warcup.fungalITS.fasta | sed sed 's/>//' > Warcup.fungalITS.taxonomy.tsv

3) import taxonomy:

qiime tools import \
    --input-path Warcup.fungalITS.taxonomy.tsv \
    --type 'FeatureData[Taxonomy]' \
    --input-format 'HeaderlessTSVTaxonomyFormat' \
    --output-path Warcup-fungalITS-taxonomy.qza

4) import FASTA:

qiime tools import \
    --input-path Warcup.fungalITS.fasta \
    --type 'FeatureData[Sequence]' \
    --output-path Warcup-fungalITS-seqs.qza

5) train classifier

qiime feature-classifier fit-classifier-naive-bayes \
    --i-reference-reads Warcup-fungalITS-seqs.qza \
    --i-reference-taxonomy Warcup-fungalITS-taxonomy.qza \
    --o-classifier Warcup-fungalITS-classifier.qza

I think this should get you started.

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