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Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. [see: Kraken 1's Webpage for more details].
Kraken 2 provides significant improvements to Kraken 1, with faster database build times, smaller database sizes, and faster classification speeds. These improvements were achieved by the following updates to the Kraken classification program:
- Storage of Minimizers: Instead of storing/querying entire k-mers, Kraken 2 stores minimizers (l-mers) of each k-mer. The length of each l-mer must be ≤ the k-mer length. Each k-mer is treated by Kraken 2 as if its LCA is the same as its minimizer's LCA.
- **Introduction of Spaced Seeds: **Kraken 2 also uses spaced seeds to store and query minimizers to improve classification accuracy.
- Database Structure: While Kraken 1 saved an indexed and sorted list of k-mer/LCA pairs, Kraken 2 uses a compact hash table. This hash table is a probabilistic data structure that allows for faster queries and lower memory requirements. However, this data structure does have a <1% chance of returning the incorrect LCA or returning an LCA for a non-inserted minimizer. Users can compensate for this possibility by using Kraken's confidence scoring thresholds. 4. Protein Databases: Kraken 2 allows for databases built from amino acid sequences. When queried, Kraken 2 performs a six-frame translated search of the query sequences against the database.
- 16S Databases: Kraken 2 also provides support for databases not based on NCBI's taxonomy. Currently, these include the 16S databases: Greengenes, SILVA, and RDP.
The Kraken 2 paper has been published in Genome Biology as of November 28th, 2019:Improved metagenomic analysis with Kraken 2 (2019).
The original Kraken paper was published in Genome Biology in 2014: Kraken: ultrafast metagenomic sequence classification using exact alignments.
The following tools are compatible with both Kraken 1 and Kraken 2. Both tools are designed to assist users in analyzing and visualizing Kraken results.
Bracken allows users to estimate relative abundances within a specific sample from Kraken 2 classification results. Bracken uses a Bayesian model to estimate abundance at any standard taxonomy level, including species/genus-level abundance.
Pavian has also been developed as a comprehensive visualization program that can compare Kraken 2 classifications across multiple samples.
Derrick Wood
For technical issues, bug reports, and code contributions, please submit a github issue Page Updated: 2020/03/04