Request for a KrakenUniq + Bracken + Krona workflow

[pcantalupo]

Description of feature

Hello, I'm working on a tumor microbiome study following Ge et al. 2025 (https://doi.org/10.1126/scitranslmed.ads6335) which uses KrakenUniq with the Microbial2023 index (https://benlangmead.github.io/aws-indexes/k2). The index is specific for KrakenUniq and does not work with Kraken2.

The problem is when I run the pipeline with --run_krakenuniq the output doesn't feed into Bracken or Krona visualization. Is there a way to enable KrakenUniq/Bracken/Krona in the pipeline? I tested Bracken v3.1 and it works directly with KrakenUniq reports. I think support for this started in Bracken v2.8 https://github.com/jenniferlu717/Bracken/releases/tag/v2.8

For background, my study is for low biomass metastatic tumor samples where contamination filtering is critical. So, I need unique k-mer counting alongside accurate abundance estimation with bracken.

[jfy133]

Thanks for the suggestion @pcantalupo !

On reflection I realise this might require larger reworking than I initial expected as we will have to generate more test databases (also update #createtaxdb in parallel, which has been a HUGE pain in the butt), and duplicate the kraken2 workflow including supporting both krakenuniq and bracken parameters in the same db_params column. It may take some time to get to.