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khyox / recentrifuge

Recentrifuge: robust comparative analysis and contamination removal for metagenomics
http://www.recentrifuge.org
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centrifuge db #4

Closed shlomobl closed 6 years ago

shlomobl commented 6 years ago

Hi,

How may I use for recentrifuge the same libraries/db that I already downloaded for centrifuge?

Thanks!

khyox commented 6 years ago

Recentrifuge only needs to know the path of the NCBI nodes information files (nodes.dmp and names.dmp) that were used when the Centrifuge DB was created, but any newer release of these files should also work fine. You can indicate such path to Recentrifuge by the flag -n PATH or --nodespath PATH. Alternatively, you can execute retaxdump.py. It will download and unzip the required local databases from NCBI servers under the subdirectory taxdump.

shlomobl commented 6 years ago

Thanks. What about the sequences themselves. I downloaded the prebuilt indexes for nt dabatase from the Centrifuge site. Can I use this file too?

khyox commented 6 years ago

Sure! Recentrifuge will read the Centrifuge output, independently of the DB that you use for the taxonomic classification. Just follow the instructions in the wiki.

khyox commented 6 years ago

I am closing this. Please reopen if there are further related questions.