| name | kraken2 |
| description | k-mer taxonomic classification; pair with Bracken for abundance. Use this skill when working with kraken2: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/DerrickWood/kraken2. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["taxonomy","k-mer","bracken"] |
| upstream | https://github.com/DerrickWood/kraken2 |
Kraken2 (+ Bracken)
Upstream: DerrickWood/kraken2 ·
Bracken: jenniferlu717/Bracken
Citation
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
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
Kraken2 classifies each read by minimizer / k-mer LCA against a database.
Sensitivity and false positives are database-dominated (RefSeq completeness,
eukaryotic host contamination in DB, custom biome DBs).
Bracken re-estimates abundances at a chosen rank from Kraken reports; it does
not validate rare taxa. MetaPhlAn 4 comparisons reported elevated false-positive
rates for some Bracken configurations — keep method-specific Results and avoid
“species X confirmed by both” unless thresholds are pre-registered.
Use Kraken2 for speed, custom DBs, or contig classification. Prefer MetaPhlAn
for marker specificity; Metabuli when joint DNA+AA classification is desired;
sylph for sketch containment against genome sets.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| DB | Built Kraken2 DB | Standard or custom; huge disk |
| RAM | Often ≥ DB size resident | 64–200 GB+ depending on DB |
| Input | FASTQ or FASTA | Dehosted preferred |
How to run
kraken2 --db $KRAKEN2_DB --paired \
temp/hr/${id}_1.fastq temp/hr/${id}_2.fastq \
--report result/kraken2/${id}.report \
--output result/kraken2/${id}.kraken \
--threads 16
bracken -d $KRAKEN2_DB -i result/kraken2/${id}.report \
-o result/kraken2/${id}.bracken -r 150 -l S
Decision tree
Classification goal?
├─ Broad/custom DNA DB → kraken2
├─ Species abundance smoothing → bracken after kraken2
├─ Marker SGBs → metaphlan
├─ Joint DNA+AA → metabuli
└─ Genome containment sketches → sylph
Related skills
bracken · metaphlan · metabuli · kaiju · sylph · visualization · tool-selection
