# Kraken2 2.1.2 ## Kraken2 taxonomic sequence classification system Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. Kraken examines the k-mers within a query sequence and uses the information within those k-mers to query a database. That database maps k-mers to the lowest common ancestor (LCA) of all genomes known to contain a given k-mer. The first version of Kraken used a large indexed and sorted list of k-mer/LCA pairs as its database. While fast, the large memory requirements posed some problems for users, and so Kraken 2 was created to provide a solution to those problems. Kraken 2 differs from Kraken 1 in several important ways: 1. Only minimizers of the k-mers in the query sequences are used as database queries. Similarly, only minimizers of the k-mers in the reference sequences in the database's genomic library are stored in the database. We will also refer to the minimizers as ℓ-mers, where ℓ ≤ k. All k-mers are considered to have the same LCA as their minimizer's database LCA value. 2. Kraken 2 uses a compact hash table that is a probabilistic data structure. This means that occasionally, database queries will fail by either returning the wrong LCA, or by not resulting in a search failure when a queried minimizer was never actually stored in the database. By incurring the risk of these false positives in the data structure, Kraken 2 is able to achieve faster speeds and lower memory requirements. Users should be aware that database false positive errors occur in less than 1% of queries, and can be compensated for by use of confidence scoring thresholds. 3. Kraken 2 has the ability to build a database from amino acid sequences and perform a translated search of the query sequences against that database. 4. Kraken 2 utilizes spaced seeds in the storage and querying of minimizers to improve classification accuracy. 5. Kraken 2 provides support for "special" databases that are not based on NCBI's taxonomy. These are currently limited to three popular 16S databases. Location and version: ```console $ which kraken2 /local/cluster/bin/kraken2 $ kraken2 --version Kraken version 2.1.2 Copyright 2013-2021, Derrick Wood (dwood@cs.jhu.edu) ``` help message: ```console $ kraken2 --help Usage: kraken2 [options] Options: --db NAME Name for Kraken 2 DB (default: none) --threads NUM Number of threads (default: 1) --quick Quick operation (use first hit or hits) --unclassified-out FILENAME Print unclassified sequences to filename --classified-out FILENAME Print classified sequences to filename --output FILENAME Print output to filename (default: stdout); "-" will suppress normal output --confidence FLOAT Confidence score threshold (default: 0.0); must be in [0, 1]. --minimum-base-quality NUM Minimum base quality used in classification (def: 0, only effective with FASTQ input). --report FILENAME Print a report with aggregrate counts/clade to file --use-mpa-style With --report, format report output like Kraken 1's kraken-mpa-report --report-zero-counts With --report, report counts for ALL taxa, even if counts are zero --report-minimizer-data With --report, report minimizer and distinct minimizer count information in addition to normal Kraken report --memory-mapping Avoids loading database into RAM --paired The filenames provided have paired-end reads --use-names Print scientific names instead of just taxids --gzip-compressed Input files are compressed with gzip --bzip2-compressed Input files are compressed with bzip2 --minimum-hit-groups NUM Minimum number of hit groups (overlapping k-mers sharing the same minimizer) needed to make a call (default: 2) --help Print this message --version Print version information If none of the *-compressed flags are specified, and the filename provided is a regular file, automatic format detection is attempted. ``` Databases will be maintained in: `/nfs1/CGRB/databases/kraken2/current/` [Link to manual](../docs/kraken2/MANUAL.html) software ref: software ref: research ref: