kraken2

Taxonomic sequence classification system for DNA/RNA reads

brewmacoslinux

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Taxonomic sequence classification system

kraken2kraken2-buildkraken2-inspect

Classify metagenomic reads against a standard database$ kraken2 --db /path/to/database --threads 4 reads.fastq > results.txt

Build a custom Kraken2 database from reference sequences$ kraken2-build --download-taxonomy --db custom_db

Generate a report of taxonomic classifications$ kraken2 --db /path/to/database reads.fastq --report report.txt --output output.txt