Update readthedocs links. Move text around.

README.md

@@ -1,32 +1,38 @@
 # Canu
 
-<img style="float: left; margin: 50px 50px;" align=left src="https://raw.githubusercontent.com/marbl/canu/master/logo.jpg" width="125" /> Canu is a fork of the [Celera Assembler](http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page "Celera Assembler") designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.
+<img style="float: left; margin: 50px 50px;" align=left src="https://raw.githubusercontent.com/marbl/canu/master/logo.jpg" width="125" />
 
-## Build
+Canu is a fork of the [Celera Assembler](http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page), designed for high-noise single-molecule sequencing (such as the [PacBio](http://www.pacb.com) [RS II](http://www.pacb.com/products-and-services/pacbio-systems/rsii/) or [Oxford Nanopore](https://www.nanoporetech.com/) [MinION](https://www.nanoporetech.com/products-services/minion-mki)).
+
+Canu is a hierachical assembly pipeline which runs in four steps:
+
+* Detect overlaps in high-noise sequences using [MHAP](https://github.com/marbl/MHAP)
+* Generate corrected sequence consensus
+* Trim corrected sequences
+* Assemble trimmed corrected sequences
+
+## Build:
 
     git clone https://github.com/marbl/canu.git
     cd canu/src
     make -j <number of threads>
-
-For a quick user-quide, run:
+
+## Run:
+
+Brief command line help:
 
     ../<achitechture>/bin/canu
 
 
-For full list of options, run:
+Full list of parameters:
 
     ../<architecture>/bin/canu -options
 
-## Docs
-Canu is a hierachical assembly pipeline which runs in four steps:
+## Learn:
 
-* Detect overlaps in high-noise sequences using [MHAP](https://github.com/marbl/MHAP "MHAP")
-* Generate corrected sequence consensus
-* Trim corrected sequences
-* Assemble trimmed corrected sequences
+The [quick start](http://canu.readthedocs.io/en/stable/quick-start.html) will get you assembling quickly, while the [tutorial](http://canu.readthedocs.io/en/stable/tutorial.html) explains things in more detail.
 
-Read the [documentation](http://canu.readthedocs.org/ "docs")
+## Citation:
 
-## Citation
- - Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM [Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing](http://www.nature.com/nbt/journal/v33/n6/abs/nbt.3238.html "nb"). Nature Biotechnology. (2015).
+ - Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM [Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing](http://www.nature.com/nbt/journal/v33/n6/abs/nbt.3238.html). Nature Biotechnology. (2015).
  - Stay tuned for a Canu-specific citation