Question: Adding Custom genomes in Kraken
gravatar for Ron
3.7 years ago by
United States
Ron1000 wrote:

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 :

But the terminology they mean is a bit confusing.These are the files in my Viruses directory.




rna-seq kraken next-gen viruses • 2.3k views
ADD COMMENTlink written 3.7 years ago by Ron1000

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:

kraken-build --add-to-library chr1.fa --db $DBNAME

In your case, that would be viral.2.1.genomic.fna.

ADD REPLYlink written 3.7 years ago by igor11k

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?

ADD REPLYlink written 20 months ago by xingpeng_li0
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