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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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No taxonomic annotations provided #62

Closed xapple closed 9 years ago

xapple commented 9 years ago

So I have a bunch of contigs (that were assembled from a environmental shotgun metagenome) and would like to have some taxonomical annotations assigned to them. It seems like prokka is a program that can provide this. However, I was not able to retrieve any such information. I have tried different options such as --usegenus or --kingdom Bacteria or no options at all. Invariably, every sequence in the resulting .fsa file will include the following uninformative header:

>contig-0000001 [gcode=11] [organism=Genus species] [strain=strain]

What is one supposed to do to get taxonomical annotations ?

aleimba commented 9 years ago

Prokka is really not the right tool for this job, it's for annotating prokaryotic contigs/replicons and that's it.

I'm definitely not an expert on that field, but I think most of the metagenomics crowd use the reads from the NGS machine directly (after QC, adapter trimming etc. of course) to do the taxonomic classification. A good tool for that is Kraken from the Salzberg group (http://ccb.jhu.edu/software/kraken/).

If you want to assign your assembled contigs @nickloman has a blog post including these: http://pathogenomics.bham.ac.uk/blog/2013/08/methods-for-taxonomic-assignment-of-shotgun-whole-genome-metagenomics-reads/

You can also use blobology (which I have used for QC): https://github.com/blaxterlab/blobology

In the end, I recommend to shop around in http://seqanswers.com/, https://www.biostars.org/, PubMed etc.

xapple commented 9 years ago

Hey thanks a lot for the info ! I will check that out.