Kraken 2 is an improved version of Kraken, a tool for metagenomic sequence classification. Kraken 2 reduces memory usage by 85% compared to Kraken 1, allowing for larger reference genomic data sets while maintaining high accuracy and increasing classification speed by five times. It introduces a translated search mode, enhancing sensitivity in viral metagenomics analysis. Kraken 2 uses a probabilistic, compact hash table to map minimizers to lowest common ancestor (LCA) taxa, reducing memory usage. The tool also features a spaced seed searching scheme and automated masking of low-complexity reference sequences. Evaluations show that Kraken 2 exhibits similar or superior accuracy to other nucleotide classifiers and comparable performance to translated search classifiers like Kaiju. Kraken 2 is compatible with the Bracken software for species-level sequence abundance estimation. The tool's memory efficiency and improved algorithms make it suitable for large-scale metagenomic studies.Kraken 2 is an improved version of Kraken, a tool for metagenomic sequence classification. Kraken 2 reduces memory usage by 85% compared to Kraken 1, allowing for larger reference genomic data sets while maintaining high accuracy and increasing classification speed by five times. It introduces a translated search mode, enhancing sensitivity in viral metagenomics analysis. Kraken 2 uses a probabilistic, compact hash table to map minimizers to lowest common ancestor (LCA) taxa, reducing memory usage. The tool also features a spaced seed searching scheme and automated masking of low-complexity reference sequences. Evaluations show that Kraken 2 exhibits similar or superior accuracy to other nucleotide classifiers and comparable performance to translated search classifiers like Kaiju. Kraken 2 is compatible with the Bracken software for species-level sequence abundance estimation. The tool's memory efficiency and improved algorithms make it suitable for large-scale metagenomic studies.