create NCBI database

[thedam (Damian Loska)]

Hey,
I'd like to use NCBI database for classification. I can find taxonomy/sequences for Silva and GreenGenes, but there's no any hints how to create such NCBI-based database.

Any suggestion how to perform it? Should I download all bacteria sequences one-by-one or there are already some tricks how to do it fast?

Thanks

[ben (benjamin w.)]

Hi Damian, hope all is well, there's some threads on this:

Feature-classifier with Blast reference dataset

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…

BLAST+ taxonomy classifier

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

[thedam (Damian Loska)]

Great, thanks, I'll have a look on that!.
I don't want to use GreenGeenes as it's 6 years old now ;(

[ben (benjamin w.)]

Yeah, the lab still uses greengenes as some of the inferred metagenome is connected to greengenes annotations. Ben

[Peter_Kos]

Hi,
did you manage to find/create the NCBI 16S Fasta file(s) and a respective taxonomy file?
I would also be happy to test the native (original) NCBI database, as that should be the authentic and most recent reference.
Moreover I find contradictory items in Silva132 like
"k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Stramenopiles
D_0__Bacteria;D_1__Proteobacteria;D_2__Gammaproteobacteria;D_3__Betaproteobacteriales"
that I do not really know what to think about.

[SoilRotifer (Mike Robeson)]

Hi @Peter_Kos,

The new SILVA v138 reference database recently became available. There should be a QIIME compatible version soon, with less messy taxonomy. My recent attempt to making a cleaner taxonomy is available here:

Silva classifier seven level code

Hi all, just an FYI: Here are new locations for the updated SILVA taxonomy (i.e. Greengenes-like) reference files for both the SSU and LSU data. To save space and bandwidth, these are the raw FASTA and TSV files. So, you’ll have to import and train them yourself. Be sure to read the SILVA License. Be wary of the species labels. For example, there are a few taxa annotated with a species label that corresponds not to the organism to which the sequence belongs, but from the source material from w…

Other details are outlined in the rest of the above thread as well this one:

Why all taxonomic levels on BarPlot have 'D' letter?

I can likely provide some insight here as I am one of the contributors that helped to format SILVA database for QIIME. The D_X__ convention was chosen to be as much of a unique and "safe" text string as possible, considering many of the bizarre taxonomy text annotations within the SILVA reference database. That is, it was meant as a quick fix to be able to search and parse these taxonomy strings. The 'D' was a way of annotating the "taxonomic Depth". At the time some of the code was written, th…

-Mike

[SoilRotifer (Mike Robeson)]

Regarding this:

“k__Bacteria;p__ Cyanobacteria;c__Chloroplast ;o__Stramenopiles

See:

Mitochondrial 16S handling

Hi @Alban_OTT, It is definitely true that you will sometimes see organelle rRNA sequences in your data, and they will often be classified during taxonomy classification. For example, in Greengenes, mitochondrial rRNA are often classified as: k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; ... and chloroplast rRNA are often classified as: k__Bacteria; p__Cyanobacteria; c__Chloroplast; .... (Chloroplasts descend from Cyanobacteria, and mitochondria f…

We often recommend removing these sequences prior to analysis.

-Mike