Curating fungal analysis with BLAST

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#1

Hello all, I have fungal data that I have assigned taxonomy to using the UNITE database. The assignments are pretty good down to the genus level for the most prevalent ASVs, but some of the most frequent ASVs have unfortunately been assigned to unidentified genera (eg, k__Fungi;p__Basidiomycota;c__Malasseziomycetes;o__Malasseziales;f__Malasseziaceae;g__unidentified).

Thus, I am hoping to manually assign taxonomy to these sequences using BLAST. My question is the following: after assigning taxonomy to these sequences of interest using BLAST, where in the QIIME pipeline analysis process could I plug in these adjustments (eg, to repseqs.qza, to taxonomy.qza). Is this even something that I can do in QIIME? If not, any ideas on how I would do this?

Thanks so much!

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#2

Hello Hunter,

Not easily, and perhaps for good reason. This 'two-phase manual blast annotation' will be difficult (or impossible!) for future researchers to replicate, so while it may improve taxonomy for some ASVs, it could also cause a lot of confusion.

(And if I'm worried about this, then you know reviewer three is going to have questions :exploding_head: )

If you want to do it anyway, here's the process:

Export your taxonomy.qza as a .biom file, convert that to a tsv file, edit the ASVs with new taxonomy from blast, then import that back into a Qiime2 taxonomy_edited.qza file.

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#3

Thank you, Colin. That makes sense. In this case, I won't be pursuing this, but thank you for your explanation.

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