ben
November 29, 2019, 2:50pm
2
Hi Damian, hope all is well, there's some threads on this:
Yes. Any fasta sequence data, in fact, can be used (with accompanying taxonomy in the same format used by greengenes). Once it is imported as a QIIME2 FeatureData[Sequence] artifact.
The reason: classify-consensus-blast is NOT the same as NCBI BLAST. Read the paper that @Mehrbod_Estaki linked to — the classify-consensus-* methods wrap an alignment algorithm (blast+ or vsearch) for database searching, but then use a LCA method to find consensus taxonomy. So the same underlying algorithm for dat…
Hi @microbiomeAnalyst ,
Good questions!
Sure, if those are the sequences you want to taxonomically classify.
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 th…
Personally, I haven't used these methods, but briefly looking through these archived threads (and one more recently), it's not different than using the 16S gene databases (which I am most familiar with greengenes). It looks like you will have to do some work to get it working. Ben
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