README.history

The Celera Assembler Source Code
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Software Background

The Celera Assembler [Myers 2000] was designed to reconstruct mammalian 
chromosomal DNA sequences from the short fragments of a whole genome shotgun 
sequencing project. The Celera Assembler was used to produce reconstructions of 
several large genomes, namely those of Homo sapiens [Venter 2001], Mus musculus 
[Mural 2002], Rattus norvegicus [unpublished data], Canis familiaris [Kirkness 
2003], Drosophila melanogaster [Adams 2000], and Anopheles gambiae [Holt 2001]. 
The Celera Assembler was shown to be very accurate when its reconstruction of 
the human genome was compared to independent reconstructions completed later 
[Istrail 2004]. 

The Celera Assembler is a pipeline consisting of several executable programs. 
The source code includes programs in the C language with Unix make scripts. The 
program was designed to run under Compaq(R) Tru64(R) Unix with access to 32GB 
RAM. It has also run under IBM(R) AIX(R) and Red Hat Linux. The latest version 
of the Celera Assembler source code is distributed on CD on an "as-is" basis.

Software Availability

As a supplement to the publication [Istrail 2004], Celera and Applied Biosystems 
are making the Celera Assembler available under the terms and conditions of the 
GNU General Public License, version 2, as published by the Free Software 
Foundation. This license allows unrestricted use of the software subject to 
provisions designed to ensure that any modifications or distributions of the 
software remain in the public domain. For more information, see 
http://www.gnu.org/copyleft/gpl.html

References

Adams et al. (2000) The Genome Sequence of Drosophila melanogaster. Science 287 2185-2195.
Holt et al. (2002) The Genome Sequence of the Malaria Mosquito Anophelesd gambiae. Science 298 129-149.
Istrail et al. (2004) Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies. PNAS 101 1916-1921.
Kirkness et al. (2003) The Dog Genome: Survey Sequencing and Comparative Analysis. Science 301 1898-1903.
Mural et al. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science 296 1661-1671.
Myers et al. (2000) A Whole-Genome Assembly of Drosophila. Science 287 2196-2204.
Venter et al. (2001) The Sequence of the Human Genome. Science 291 1304-1351.