Entering edit mode
7.2 years ago
Ron
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1.2k
Hi all,
I have installed kraken successfully and have been able to run on the standard genomes it provides : Bacteria,Viruses. But I looked at the results and it does not report quantification for most viruses,so I would like to add the viruses in the database.
I looked at the manual here : http://ccb.jhu.edu/software/kraken/MANUAL.html#custom-databases
But the terminology they mean is a bit confusing.These are the files in my Viruses directory.
lib.complete,viral.2.1.genomic.fna,viral.2.genomic.gbff,viral.2.protein.faa,viral.2.protein.gpff
Thanks,
Ron
Which part is confusing? They mention different options, so not every command is relevant.
Kraken is basically expecting a set of FASTA files that you can add one at a time as the example shows:
In your case, that would be
viral.2.1.genomic.fna
.In this case, what if the fasta file did not have a taxid? For example, the viral genome did not have a formal scientific name in NCBI? It there a way to add the sequence without taxid in the database?