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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Downloading vertebrate_mammalian kraken2 database? #668

Closed danarte closed 1 year ago

danarte commented 1 year ago

I saw there is no premade reference database available for kraken 2 that includes vertebrate. I found a thread talking about downloading the vertebrate_mammalian/ database from NCBI but it was closed without an answer.

Is it possible to download said database using the kraken package? If no, what would be the correct way to prepare those sequences for a kraken database?

danarte commented 1 year ago

I was able to download the database. It requires applying two fixes mentioned in those threads: https://github.com/DerrickWood/kraken2/pull/324/commits/f8f71b229ae6d39cbf00ea6d27a7abf2f85e9281 https://github.com/DerrickWood/kraken2/issues/292#issuecomment-1206837801