Celera Assembler
Overview
Celera Assembler is scientific software for DNA research. It can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing. The Celera Assembler enabled many advances in genomics, including the first genome sequence of a multi-cellular organism and the first diploid sequence of an individual human.
The Celera Assembler is a member of a class of software called whole-genome shotgun assemblers. The Celera Assembler is mature, efficient, open-source software with a long record of contributions to science. Celera Assembler is written mostly in C for unix operating systems. Although it requires large compute resources to resolve complex genomes, it can assemble bacterial genomes on a laptop.
This important software is an "open source" project. Originally developed at Celera Genomics, it was released under the GNU Public License and deposited on a public repository (Source Forge) in 2004. Scientists around the world can download, build, and run the software without restriction. In addition, they can inspect the source code and alter it at their own sites. Workers at JCVI and a few other institutes regularly submit their code alterations to the public repository.
JCVI has made many important contributions to Celera Assembler. Scientists and engineers at JCVI are extending the code to handle more and more polymorphic data sets, including environmental samples. In collaboration with scientists at the University of Maryland, they are adding the capability to assemble pyrosequencing data (as from a 454 FLX machine) in addition to the traditional Sanger sequencing data (as from an ABI 3730 machine). JCVI's efforts provide the cutting edge software that genome scientists around the world will need as they apply DNA sequencing technology to more and more difficult problems of biology.
Funding
This work is supported by the National Insitutes of Health (NIH) including the National Institute of Allergy and Infectious Disease (NIAID) and the National Institute of General Medical Sciences (NIGMS).