Your message dated Sun, 19 May 2019 19:00:10 +0000
with message-id <e1hsr2y-0003ed...@fasolo.debian.org>
and subject line Bug#924567: fixed in kraken2 2.0.7~beta-1
has caused the Debian Bug report #924567,
regarding ITP: kraken2 -- taxonomic classification system using exact k-mer
matches
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
924567: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=924567
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Subject: ITP: kraken2 -- taxonomic classification system using exact k-mer
matches
Package: wnpp
Owner: Andreas Tille <ti...@debian.org>
Severity: wishlist
* Package name : kraken2
Version : 2.0.7~beta
Upstream Author : Derrick Wood <dw...@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
--- End Message ---
--- Begin Message ---
Source: kraken2
Source-Version: 2.0.7~beta-1
We believe that the bug you reported is fixed in the latest version of
kraken2, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 924...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated kraken2 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 14 Mar 2019 14:13:17 +0100
Source: kraken2
Binary: kraken2
Architecture: source amd64
Version: 2.0.7~beta-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
kraken2 - taxonomic classification system using exact k-mer matches
Closes: 924567
Changes:
kraken2 (2.0.7~beta-1) unstable; urgency=low
.
* Initial release (Closes: #924567)
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