| name | bracken |
| description | Bayesian re-estimation of abundance from Kraken2 reports. Use this skill when working with bracken: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/jenniferlu717/Bracken. For stage routing use tool-selection / metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["taxonomy","kraken","abundance"] |
| upstream | https://github.com/jenniferlu717/Bracken |
| stage | taxonomy |
Bracken
Upstream: Bracken
Citation
Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104 (2017). https://doi.org/10.7717/peerj-cs.104
See also docs/references.md.
Analytical thinking
Bracken redistributes Kraken-classified reads to a target taxonomic level using
a Bayesian model conditioned on genome lengths / k-mer uniqueness in the same
database build. It answers: “given Kraken’s read assignments, what are smoothed
abundances at rank L?” — not “is species X truly present?”
Caveats:
- Must use a Bracken index built from the same Kraken2 DB.
-r read length should match sequencing.- Rare taxa remain false-positive-prone; MetaPhlAn papers have criticized high
FP rates for some Bracken setups — report confidence/thresholds carefully.
- Never paste Bracken and MetaPhlAn columns into one “species abundance” matrix
without a method factor.
How to run
bracken -d $KRAKEN2_DB -i temp/kraken/${id}.report \
-o temp/kraken/${id}.bracken -r 150 -l S
Key parameters
| Flag | Notes |
|---|
-d | Same DB root as Kraken2 |
-r | Read length used to build Bracken files |
-l | Rank (S/G/…) |
-t | Min reads threshold (if used) — affects rare taxa |
Related skills
kraken2 · metaphlan · metabuli · visualization · tool-selection
