Package: kraken2 (2.1.3-1 and others)

[ Source: kraken2  ]

taxonomic classification system using exact k-mer matches

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:

 1. 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.
 2. Introduction of Spaced Seeds: Kraken 2 also uses spaced seeds to
    store and query minimizers to improve classification accuracy.
 3. 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.
 5. 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.

Other Packages Related to kraken2

• dep: libc6 (>= 2.34) [not arm64]

  GNU C Library: Shared libraries
  also a virtual package provided by libc6-udeb

  dep: libc6 (>= 2.38) [arm64]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, ppc64el, s390x]

  GCC support library

  dep: libgcc-s1 (>= 3.4) [riscv64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386]

• dep: libgomp1 (>= 6)

  GCC OpenMP (GOMP) support library

• dep: libstdc++6 (>= 13.1) [not arm64]

  GNU Standard C++ Library v3

  dep: libstdc++6 (>= 14) [arm64]

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: zlib1g (>= 1:1.2.6)

  compression library - runtime

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Architecture	Version	Package Size	Installed Size	Files
amd64	2.1.3-1	847.8 kB	1,971.0 kB	[list of files]
arm64	2.1.3-1+b1	829.9 kB	2,084.0 kB	[list of files]
armel	2.1.3-1	824.5 kB	1,877.0 kB	[list of files]
armhf	2.1.3-1	825.5 kB	1,741.0 kB	[list of files]
i386	2.1.3-1	856.5 kB	1,981.0 kB	[list of files]
ppc64el	2.1.3-1	844.4 kB	2,147.0 kB	[list of files]
riscv64	2.1.3-1+b1	839.4 kB	1,812.0 kB	[list of files]
s390x	2.1.3-1	837.5 kB	1,955.0 kB	[list of files]