Remove outdated readme file, add citation read, add history docs

README.citation

@@ -0,0 +1,2 @@
+Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).
+Stay tuned for a Canu-specific citation

documentation/source/history.rst

@@ -0,0 +1,45 @@
+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+[Mural 2002], Rattus norvegicus [unpublished data], Canis familiaris [Kirkness 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 The Celera Assembler codebase is no longer maintained.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
+
+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).