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. Then I realized later that the pipeline only supports a Kraken2/Bracken/Krona workflow. Is there a way to enable KrakenUniq/Bracken/Krona in the pipeline? I tested Bracken v3.1 and it works directly with KrakenUniq reports. Would using Kraken2 with --report-minimizer-data (to get unique k-mer counts similar to KrakenUniq but not exact) be the best alternative right now? 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.

Oh! I wasn't aware Bracken supports Krakenuniq input... so it's not supported yet If you can make a GitHub issue we can investigate adding it 🙂

Great, will do