Silva_132 16S database creation with RESCRIPt

[AndreaC (Andrea Colautti)]

Hi!

I want to create a database using SILVA_132, using only 16S sequences.

I have read the RESCRIPt tutorial on creating the database starting from silva, but I cannot figure out how to create it from silva 132 compared to silva 138 shown in the example. If I download the Silva_132_relase.zip folder from the link Archive, I cannot understand how to import the content into qiime2 as in the first part of the tutorial ...

instead of:

tax_slv_ssu_138.txt.gz
taxmap_slv_ssu_ref_nr_138.txt.gz
tax_slv_ssu_138.tre.gz
the sequence file:
SILVA_138_SSURef_Nr99_tax_silva_trunc.fasta.gz

what should i use ???

Thanks for your help

A.C.

[crusher083 (Valentyn Bezshapkin)]

Hi, Andrea!

Switch to SILVA 132/Exports and continue with Getting SILVA data: Hard Mode.. Use the same filenames as in the tutorial with 138 substituted with 132.

Alternatively, use inbuilt script & run command:

qiime rescript get-silva-data \
    --p-version '132' \
    --p-target 'SSURef_NR99' \
    --p-include-species-labels \
    --o-silva-sequences silva-132-ssu-nr99-seqs.qza \
    --o-silva-taxonomy silva-132-ssu-nr99-tax.qza

Cheers

[AndreaC (Andrea Colautti)]

Thanks for your help!

But if I wanted to extract the entire 16S sequence, as in the archive of the other link, how can I do?
I can only do this by selecting a sequence based on the primers used with:
qiime feature-classifier extract-reads
?

Thanks!

[crusher083 (Valentyn Bezshapkin)]

Hello Andrea,

SILVA database in the file contains full length sequences of 16S rRNA (or Small Sububnit - SSU). The further steps in the tutorial are made to optimize the performance for sequenced target region.

May I ask what is your final goal? Taxonomic classification?
If yes, you can download a trained classifier on full-length SILVA_132 from older versions of QIIME2 here.

[AndreaC (Andrea Colautti)]

SILVA 16S database

Hello, I am trying to replicate the taxonomic classification results of the V3 region of the 16S rRNA provided by another working group that used SILVA as a reference database using Qiime2. While using kraken2 with the appropriate SILVA 16S database I can obtain practically identical percentages, while on Qiime2 using the "Silva 138 99% OTUs full-length sequences" database I get completely different percentages, while from the "Silva 138 99% OTUs database from 515F / 806R region of sequences "…

my goal is to replicate metagenomic analyzes conducted on the 16s of bacteria with qiime2.

using the complete silva database with qiime I get % totally different from those provided, while if I repeat the analysis with the silva 16s database on kraken2 I can get practically identical results.

Surprised by this difference in values ​​obtained using different databases, I want to create a database with only the 16s as the kraken2 one hoping to get similar results...

Any advice?