These are release notes for Celera Assembler version 8.0, which was released on
November 5th, 2013.
This distribution package provides a stable, tested, documented version of the
software. The distribution is usable on most Unix-like platforms, and some
platforms have pre-compiled binary distributions ready for installation.
The source code package includes full source code (revision r4466), Makefiles,
and scripts. A subset of the kmer package (http://kmer.sourceforge.net/,
revision r1969), used by some modules of Celera Assembler, is included.
This package was prepared by scientists at the J. Craig Venter Institute
(http://www.jcvi.org/) with funding provided by the National Institutes of
Full documentation can be found online at http://wgs-assembler.sourceforge.net/.
Please cite Celera Assembler in publications that refer to its algorithm or its
output. The standard citation is the original paper [Myers et al. (2000) A
Whole-Genome Assembly of Drosophila. Science 287 2196-2204]. More recent papers
describe modifications for human genome assembly [Istrail et al. 2004; Levy et
al. 2007], metagenomics assembly [Venter et al. 2004; Rusch et al. 2007],
haplotype separation [Levy et al. 2007; Denisov et al. 2008], a
Sanger+pyrosequencing hybrid pipeline [Goldberg et al. 2006], native assembly
of 454 data [Miller et al. 2008], and correction and assembly of single-molecule
sequences [Koren et. al. 2012, Koren et. al. 2013]. There are links to these papers,
and more, in the on-line documentation (http://wgs-assembler.sourceforge.net/).
Compilation and Installation
Users can download Celera Assembler as source code or as pre-compiled
binaries. The source code package needs to be compiled and installed before it
can be used. The binary distributions need only be unpacked, but they are not
available for all platforms.
To use the source code, execute these commands on any unix-like platform:
% bzip2 -dc wgs-8.0.tar.bz2 | tar -xf -
% cd wgs-8.0
% cd kmer
% gmake install
% cd ..
% curl -L https://github.com/samtools/samtools/archive/0.1.19.tar.gz -o samtools.tar.gz
% tar xvzf samtools.tar.gz
% mv samtools-0.1.19 samtools
% cd samtools
% cd ../src
% cd ..
To use the binary distributions, choose a platform, download that package, then
unpack it with some unix command like this:
% bzip2 -dc wgs_8.0_MyPlatform.tar.bz2 | tar -xf -
In both cases, you can run the assembler with:
Copyright 1999-2004 by Applera Corporation. Copyright 2005-2013 by the J. Craig
Venter Institute. The Celera Assembler software, also known as the wgs-assembler
and CABOG, is open-source and available free of charge subject to the GNU
General Public License, version 2.