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Sanger String Graph Assembler

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!


1. a 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
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archive/bioinformatic_tools/sga.txt · Last modified: 2015/07/27 23:26 by ceisenhart