Software Background¶
Canu is derived from Celera Assembler, which is no longer maintained.
Celera Assembler [Myers 2000] was designed to reconstruct mammalian chromosomal DNA sequences from the short fragments of a whole genome shotgun sequencing project. 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of several large genomes, namely those of Homo sapiens [Venter 2001], Mus musculus [Mural 2002], Rattus norvegicus [unpublished data], Canis familiaris [Kirkness 2003], Drosophila melanogaster [Adams 2000], and Anopheles gambiae [Holt 2001]. 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 2012], demonstrating finished bacterial genomes [Koren 2013] and efficient algorithms for eukaryotic assembly [Berlin 2015].
Celera Assembler was released under the GNU General Public License, version 2 as a supplement to [Istrail 2004].
Canu [Koren and Walenz 2017] was branched from Celera Assembler in 2015, and specialized for single-molecule high-noise sequences. For the most recent license information on Canu, see README.licences.
References¶
- Adams et al. (2000) The Genome Sequence of Drosophila melanogaster. Science 287 2185-2195.
- 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.
- Mural et al. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science 296 1661-1671.
- 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.
- Venter et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 66-74.
- Levy et al. (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biology 0050254
- Rusch et al. (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology 1821060.
- Denisov et al. (2008) Consensus Generation and Variant Detection by Celera Assembler. Bioinformatics 24(8):1035-40
- Miller et al. (2008) Aggressive Assembly of Pyrosequencing Reads with Mates. Bioinformatics 24(24):2818-2824
- Koren et al. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, July 2012.
- Koren et al. (2013) Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology 14:R101.
- Berlin et. al. (2015) Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).
- Koren and Walenz et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017).