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documentation/source/history.rst

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 Software Background
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+--------------------
 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 
@@ -27,19 +27,19 @@ to the publication [Istrail 2004]. For the most recent license information pleas
 README.licences
 
 References
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-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).
+--------------------
+- 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).