Your message dated Fri, 24 Jul 2015 16:00:51 +0000
with message-id <[email protected]>
and subject line Bug#770063: fixed in kmc 2.0+dfsg-1
has caused the Debian Bug report #770063,
regarding ITP: kmc -- count kmers in genomic sequences
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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--
770063: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=770063
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Jorge Soares <[email protected]>
* Package name : kmc
Version : 20
Upstream Author : Sebastian Deorowicz <[email protected]>, Marek
Kokot, Szymon Grabowski, Agnieszka Debudaj-Grabysz
* URL : http://sun.aei.polsl.pl/kmc/index.html
* License : GPL3
Programming Lang: C, C++
Description : count kmers in genomic sequences
KMC—K-mer Counter is a utility designed for counting k-mers (sequences of
consecutive k symbols) in a set of reads from genome sequencing projects. K-mer
counting is important for many bioinformatics applications, e.g., developing de
Bruijn graph assemblers. Building de Bruijn graphs is a commonly used approach
for genome assembly with data from second-generation sequencer. Unfortunately,
sequencing errors (frequent in practice) results in huge memory requirements
for de Bruijn graphs, as well as long build time. One of the popular approaches
to handle this problem is filtering the input reads in such a way that unique
k-mers (very likely obtained as a result of an error) are discarded.
Thus, KMC scans the raw reads and produces a compact representation of all
non-unique reads accompanied with number of their occurrences. The algorithm
implemented in KMC makes use mostly of disk space rather than RAM, which allows
to use KMC even on rather typical personal computers. When run at high-end
server (what is necessary for KMC competitors) it outperforms them in both
memory requirements and speed of computation. The disk space necessary for
computation is in order of the size of input data (usually it is smaller).
kmc is a dependency of the iva - Iterative Virus Assembler - package
The software is used widely at the Wellcome Trust Sanger Institute
Sponsorship needed.
--- End Message ---
--- Begin Message ---
Source: kmc
Source-Version: 2.0+dfsg-1
We believe that the bug you reported is fixed in the latest version of
kmc, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Jorge Soares <[email protected]> (supplier of updated kmc 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 03 Nov 2014 14:46:54 +0200
Source: kmc
Binary: kmc
Architecture: source amd64
Version: 2.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Jorge Soares <[email protected]>
Description:
kmc - count kmers in genomic sequences
Closes: 770063
Changes:
kmc (2.0+dfsg-1) unstable; urgency=medium
.
* Initial release (Closes: #770063)
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