Silva 138 for Qiime2

[thedam (Damian Loska)]

Hey,
are there some plans to update Silva138 database for Qiime?

Archive

Cheers,
Damian

[colinbrislawn (Colin J Brislawn)]

Hello Damian,

Sounds like @SoilRotifer is going to try to import this new database!

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

Hi @colinbrislawn That is a good question! I am not associated with the SILVA folks, or am I involved with their maintenance of taxonomy. But I typically, treat these ambiguous identifiers as, i.e. “unidentified” or “ambiguous”. I’ll try and parse the new SILVA v138 DB that recently came out. I’ll post a link to these files when I get a chance. This way they will have 6 or 7-rank taxonomy labels as I’ve done for the previous 132 DB files. They are available here, until I can find a more perman…

Not sure if there is an official thread for this new database, yet!

Colin

[SoilRotifer (Mike Robeson)]

Hi @colinbrislawn & @thedam,

I’m working on this, and tweaking some of the quality control steps I use to generate this reference set. I should have something to share on this around the New Year.

-Mike

[yannreynaud]

Hi!
Thanks for working on it. Do you have news about the Silva138 for qiime2?
Best
Yann

[SoilRotifer (Mike Robeson)]

Hi @yannreynaud,

Sorry, I forgot to update ya'll in this thread. I made a new post here about a working version of SILVA 138:

SILVA 138 Classifiers

This pipeline has been vastly improved via the new RESCRIPt plugin. Which you can check out via the link below. We hope the process of constructing your own reference sequence database (e.g. SILVA) will be far less onerous.

Click here to see the original documentation

I just wanted to let everyone be aware that I've hobbled together a simple <a href="https://github.com/mikerobeson/make_SILVA_db">pipeline</a> for constructing classifiers based …

-Mike

[yannreynaud]

Hi! Thanks for answering me and for giving this SILVA138 available for the qiime2 users! All the best
Yann

[Luz_Chacon_Jimenez (Luz Chacón Jiménez)]

Thanks a lot! The files that you kindly upload are ready to use o we have to cluster it with vsearch?

[SoilRotifer (Mike Robeson)]

Hi @Luz_Chacon_Jimenez, for classifying your sequences, it’s best to make use of the files as they are, you can rebuild the classifiers yourself, or use the ones provided.

FYI, these are the NR99 clustered data from SILVA.

[SoilRotifer (Mike Robeson)]

Hi there, I just wanted to refer the everyone over to the tutorial linked below. We hope the process of constructing your own reference sequence database (e.g. SILVA) is far less onerous.

Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

Please consider this tutorial a living document, which may change based upon community feedback and ongoing plugin development. RESCRIPt RESCRIPt (REference Sequence annotation and CuRatIon Pipeline) is a python package and QIIME 2 plugin for formatting, managing, and manipulating sequence reference databases. This package was designed for compiling, manipulating, and evaluating sequence reference databases from SILVA, NCBI, Greengenes, GTDB, and other sources, and for construc…

-Best wishes!
-Mike