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DerrickWood / kraken

Kraken taxonomic sequence classification system
http://ccb.jhu.edu/software/kraken/
GNU General Public License v3.0
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Regarding custom database #18

Closed Ramanandan closed 9 years ago

Ramanandan commented 9 years ago

Dear Derrick,

Thanks for developing kraken pipeline for the scientific community. I have couple of queries regarding the kraken database. 1) I believe, currently kraken uses RefSeq genomes for bacterial, archael, viral and human. Can I include fungal, plant, nematodes sequences in the database? 2) Instead of RefSeq genomes, can I use RefSeq protein to build my custom database?

Cheers, Ram

Ramanandan commented 9 years ago

Dear Derrick,

Can you please provide some updates on the above query?

DerrickWood commented 9 years ago

Kraken supplies explicit support for bacteria, archaea, viruses, and human databases (and combinations thereof). Customized databases, including fungi, plant, or any other genomes are acceptable - you will need to supply those sequences yourself, though. Kraken only works with nucleotide sequences at present.

Ramanandan commented 9 years ago

Thanks a lot Dr. Derrick wood for answering my queries.