BLAST+ taxonomy classifier

[microbiomeAnalyst]

Hello,

I would like to employ the classification method classify-consensus-blast by following directions at [https://docs.qiime2.org/2018.6/plugins/available/feature-classifier/classify-consensus-blast/]

Below are my questions regarding running qiime2 concensus BLAST with required parameters:

1). --i-query ARTIFACT PATH FeatureData[Sequence].

Question: Do the sequences to classify taxonomically equate to rep-seqs.qza?

2). --i-reference-reads ARTIFACT PATH FeatureData[Sequence].

Question: Are they referring to BLAST reference sequences?
Question: If this is not BLAST reference sequences, then how do we point to the NCBI blast reference sequences?

3). --i-reference-taxonomy ARTIFACT PATH FeatureData[Taxonomy]

Question: Do reference taxonomy labels equate to taxonomy.qza?

I did not see any examples in the qiime2 documentation upon which to base the blast classifier.

Thank you for your patience!

[Nicholas_Bokulich]

Hi @microbiomeAnalyst,
Good questions!

@microbiomeAnalyst

Question: Do the sequences to classify taxonomically equate to rep-seqs.qza?

Sure, if those are the sequences you want to taxonomically classify.

@microbiomeAnalyst

Question: Are they referring to BLAST reference sequences?

No, this is ANY reference database in the appropriate format (see the SILVA and greengenes reference files linked to from here). Note that BLAST is the name of the algorithm used for alignment, and is not the same thing as NCBI-BLAST (a webtool implementation of BLAST). The outputs of this classifier (which performs LCA classification on top of BLAST alignment) is also not the same thing as BLAST or NCBI-BLAST.

@microbiomeAnalyst

Question: If this is not BLAST reference sequences, then how do we point to the NCBI blast reference sequences?

You could download the NCBI nt database and use that, provided you get it in the correct format (follow the examples from above).

@microbiomeAnalyst

Question: Do reference taxonomy labels equate to taxonomy.qza?

This is the reference taxonomy; see the SILVA and Greengenes taxonomy files for examples.

@microbiomeAnalyst

I did not see any examples in the qiime2 documentation upon which to base the blast classifier.

There is no example in the docs, but you can find examples on this forum by searching the archive. For example, see here for an example of how to import the reference files and use the classifier:

Identifier not present in reference taxonomy error while running classify-consensus-blast

Hello, I have generated my own custom reference fish database and am trying to use that in classify consensus-blast. I am using QIIME2 docker image 2018.2 (I haven't upgraded to 2018.6 yet..) Here is what my fasta file looks like: [image] Here is what my taxonomy file looks like (these taxonomy IDs don't necessarily match the accession numbers above): [image] Both of these files for the cytb gene have been imported as QIIME2 artifacts with no error messages qiime tools import \ --type 'F…

[microbiomeAnalyst]

Thank you for the helpful explanations! I may have a follow-up question at a later date.