is it ok to do taxonomic classification by local alignment search tool (BLAST from NCBI) for OTUs obtained from QIIME2

[Fairytale]

Hello everyone,
I’m working on taxonomy classification for fungal ITS sequecen. For some reasons, I’d like to use the basic local alignment search tool （BLAST download from NCBI) for the classification, while my OTUs were clustured using open-reference method in QIIME2 (which use the QIIME release database in UNITE). I’m not if there is any problem to do so, because the BLAST tool from NCBI uses a Full “UNITE+INSD” dataset in UNITE and QIIME2 uses a different one.

I’m not very familier with the algorthm and relationship between them and thus worried about the results.
Thank you in advance.

BEST
Fang

[SoilRotifer (Mike Robeson)]

Hi @Fairytale,

You can use either the "QIIME" or "UNITE+INSD" database for your taxonomic classification. The QIIME version is easy to import of course, you can simply follow the instructions to import the respective taxonomy and sequence files as outlined here.

As for the "UNITE+INSD" database... The data might exist as a FASTA file with the taxonomy information in the sequence headers. So, you'll want to follow the steps outlined below, in order to make a separate taxonomy and sequence file:

How do i create a taxonomic table from fasta file?

Hello everybody, I am a new QIIME2 user. I want to work with functional genes and I am starting with the nifH gene (dinitrogenase reductase) Recently, I downloaded the database (fasta file) but the database didn’t come with the taxonomic table and the database comprise only a code name and sequence: Name sequence Therefore i can’t use QIIME without a taxonomic table and I want to create a new one. I tried to find commands how to create a table on QIIME2 or search on this forum but I didn’t…

and

Any method for converting FASTA to taxonomy (txt) format for import to FeatureData[Taxonomy]?

Check out the SILVA database — in addition to the SSU database that is most commonly used, they have a LSU database, which would include 23S. What I do not know is if it is comprehensive enough for your purposes (e.g., has all the species you expect to see). I’d start there — building on an existing database is always much easier than building a new one from scratch! what do the header lines look like in that fasta? If it is something like: >sequenceID| d_Eukaryota;k_Chromista;p_Ochrophyta;c…

More relevant information can be found in the following forum posts:

Full UNITE+INSD dataset for Fungi

Hi, I was wondering about which database should we use for ITS sequence analysis, UNITE or UNITE+INSD dataset? Is the UNITE+INSD dataset stable? Secondly, I got an error while training the UNITE database qiime tools import --type 'FeatureData[Sequence]' --input-path sh_refs_qiime_ver8_dynamic_s_02.02.2019_dev.fasta --output-path unite.qza Imported sh_refs_qiime_ver8_dynamic_s_02.02.2019_dev.fasta as DNASequencesDirectoryFormat to unite.qza qiime tools import --type 'FeatureData[Taxonomy]' …

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QI…

-Cheers!
-Mike

[Fairytale]

Hi @SoilRotifer Mike,
Thank you very much for your so detailed reply. I got it. You help a lot.
Many thanks again.

Best
Fang