domains / families / science / kraken-classification

kraken-classification

separate

Classifies shotgun metagenomic reads to taxa with Kraken2's minimizer/LCA matching against a chosen reference database, then hands off to Bracken for abundance re-estimation. Covers why the database (not the algorithm) decides what can be detected, the --confidence and --minimum-hit-groups precision levers, unique-minimizer false-positive control, host-read removal, and why raw Kraken2 read counts are not abundances. Use when profiling who-is-there from shotgun reads, choosing a Kraken2 database, setting a confidence threshold, controlling false positives, or feeding reports to Bracken. For marker-gene profiling see metaphlan-profiling; for abundance mechanics see abundance-estimation; for assembly/MAG recovery see genome-assembly/metagenome-assembly.

When to use

• profiling who-is-there from shotgun reads
• choosing a Kraken2 database
• setting a confidence threshold
• controlling false positives
• feeding reports to Bracken
• read-based taxonomic classification
• Bracken handoff
• host-read removal

When not to use

• marker-gene profiling
• abundance mechanics
• assembly/MAG recovery
• host removal and read QC
• contamination controls
• Amplicon/16S

Skill page

Source