[Debian-med-packaging] Bug#924567: ITP: kraken2 -- taxonomic classification system using exact k-mer matches

[Andreas Tille]

Package: wnpp
Severity: wishlist

Subject: ITP: kraken2 -- taxonomic classification system using exact k-mer matches
Package: wnpp
Owner: Andreas Tille <tille at debian.org>
Severity: wishlist

* Package name    : kraken2
  Version         : 2.0.7~beta
  Upstream Author : Derrick Wood <dwood at cs.jhu.edu>
* URL             : https://www.ccb.jhu.edu/software/kraken2/
* License         : GPL-3+
  Programming Lang: C
  Description     : 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.

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/kraken2