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Adding Custom genomes in Kraken

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

rna-seq next-gen viruses kraken
• 4,822 views • link
written by Ron 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:

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

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

• 0 views • link
written by igor igor

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?

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written by xingpeng_li • xingpeng_li

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