classification of non-overlapping reads treated with justConcatenate

[SoilRotifer (Mike Robeson)]

Wow this is great @lukasbeule, thank you for sharing this!

I agree that the initial results you've obtained with sklearn are what we expected. I hope the N length you have chosen works reasonable well across most taxa. However, as per:

@lukasbeule

This tells me that VSEARCH cannot handle Ns because all subsets that were concatenated by at least 1 N were classified as Unassigned .

I've discussed this previously with some of the other forum moderators, and I had forgotten to clarify in my reply to you, that vsearch may only work if the N region is a reasonable length (otherwise the global alignment would score really badly).

One minor suggestion, we have updated SILVA 138 classifiers available on the Data Resources page. Both pre-made classifiers and the files used to make them are there. If you'd like to curate your own SILVA database, you can give RESCRIPt a try:

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…

-Cheers!
-Mike