Adding nt_core db to Bracken and related workflow tools

usegalaxy.eu support
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Hello,

I have used Kraken2 with the nt_core database to classify bacteria as well as the metazoa I need. I want to use Bracken. However, the nt_core database is not an option. I selected the PlusPF (Version 2024-01-12, k-mer: 35, read: 100) for use with Bracken. However, I am concerned with inconsistencies and inaccuracies in the results due to mismatched k-mer distributions in the databases. May the nt_core database be added to Bracken?

Best regards,
Laura

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Additionally, I would like to use Kraken-filter to filter by confidence score. The nt_core database is not an option for this tool either. How would choosing the bacteria database impact my results? Is it possible to add the nt_core as an option here too?

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Hi Laura,

Yes, these all should be paired up as far as I know. Let’s ask @bjoern.gruening – are these requests enough detail or would you like a ticket?

Thanks! :slight_smile:

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Thanks jennaj! @bjoern.gruening let me know if there is anything else I need to do.

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Hi @Laura_Peirson I’ve created a ticket for the request to help the administrators keep this organized and specific. :hammer_and_wrench:

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Thank you!

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Could the core_nt reference DB also be added to the following tools:

Kraken taxonomic report
Kraken-report

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I’ve added these to the ticket Laura. If you have a Github account, also please feel free to add in more details whenever I share a link to a ticket! Or just let us know here and I or someone else from the project team can help of course.

We are open source so … our scientist users getting involved is exactly what we like.

Thanks for the great ideas to get this new db resource filled out everywhere. :scientist: