Question: How to query the taxa IDs/GIs of a kraken database
gravatar for d.hand
18 months ago by
d.hand0 wrote:

I built a database from refSEQ in December, but my hits are missing a obvious genome.

Is there any easy way to extract a list of GIs used in the construction of a database or is this logged somewhere? Is there anyway to find out what subset of refseq kraken has built from?

sequencing • 579 views
ADD COMMENTlink written 18 months ago by d.hand0

Did you find the way to extract the list of GIs from the Kraken DB? We are using as well one of the older versions of Kraken, and the only files we have are database files

ADD REPLYlink written 10 weeks ago by homeveg0
gravatar for Sej Modha
18 months ago by
Sej Modha4.2k
Glasgow, UK
Sej Modha4.2k wrote: file in the Kraken DB directory contains the seqID and the taxonomy ID as two columns. If a database was built from scratch then the fasta files should be available in the library/added/*.fna in the Kraken DB folder.

ADD COMMENTlink modified 18 months ago • written 18 months ago by Sej Modha4.2k

What version of kraken are your using? I cannot find this fille, I'm using the standard build database which produces these fills:

database.kdb database.idx taxonomy/nodes.dmp taxonomy/names.dmp:

ADD REPLYlink modified 18 months ago • written 18 months ago by d.hand0
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