====== Sanger String Graph Assembler ======
  * Written by [[http://people.pwf.cam.ac.uk/js779/|Jared Simpson]].
  * Currently only has a [[https://github.com/jts/sga|GitHub repository]].
  * Paper: Efficient construction of an assembly string graph using the FM-index [(cite:string_graph>Jared T. Simpson and Richard Durbin. Efficient construction of an assembly string graph using the FM-index. Bioinformatics 2010, 26(12): i367-i373. doi: [[http://dx.doi.org/10.1093/bioinformatics/btq217]])]

===== Methods ======
  * Uses the Burrows-Wheeler Transform(BWT)/Ferragina—Manzini(FM)-index to build a string graph.

===== String Graphs ======
  * Nodes are reads (reads that are substrings are condensed into superstrings).  Edges are overlaps between reads, and the non-overlapping prefix is stored in the forward edge and suffix is stored in the backwards edge.
  * Condenses repeats like a de Bruijn graph.
  * More expensive to construct than a de Bruijn graph.

===== BWT/FM-index =====
  * Like BWA, it uses the FM-index, which is a compressed method of inferring the suffix array.
  * The Burrows Wheeler transform B_X is an array of the last characters in the alphabetically sorted suffix array.
  * The FM-index (two data structures: 1. C_X(a) be the number of symbols in X that are lexographically lower than the symbol a, 2. Occ_X(a, i) be the number of occurrences of the symbol a in B_X[1, i], the ) allows substring searching and can be extended to construct the string graph.
===== String Graph Construction with the FM-index =====
===== Installation =====
Installation of SGA from the GitHub is a major pain, because it has so many dependencies.  It needs
  * google-sparsehash (also needed for Abyss)
  * hoard
  * bamtools, which is a particular pain to install because it uses
    * cmake (newer than the version installed on campusrocks), and cmake does not support installing stuff anywhere other than in the initial directory or root-access-only directories, so we can't do the usual "configure --prefix=/campusdata/BME235"

Once cmake, bamtools, hoard, and google/sparsehash are all installed as best they can be, then the UCSC-install.bash script can be run to install SGA.  Actually running SGA is still to be tested!