Software Background

Canu is derived from the Celera Assembler. 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of several large genomes, namely those of Homo sapiens [Venter 2001], Mus musculus [Mural 2002], Rattus norvegicus [unpublished data], Canis familiaris [Kirkness 2003], Drosophila melanogaster [Adams 2000], and Anopheles gambiae [Holt 2001].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]. It was used to reconstructing one of the first large-scale metagenomic projects [Venter 2004, Rusch 2007] and a diploid human reference [Levy 2007, Denisov 2008]. It was adapted to 454 Pyrosequencing [Miller 2008] and PacBio sequencing [Koren 2011], demonstrating finished bacterial genomes [Koren 2013] and efficient algorithms for eukaryotic assembly [Berlin 2015].

In 2015 Canu was forked from Celera Assembler and specialized for single-molecule high-noise sequences. The Celera Assembler codebase is no longer maintained.

Canu is a pipeline consisting of several executable programs and perl driver scripts. The source code includes programs in the C++ language with Unix make scripts. The original Celera Assembler 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 Celera Assembler was released under the GNU General Public License, version 2 as as supplement to the publication [Istrail 2004]. For the most recent license information please see README.licences


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