archive:bioinformatic_tools:sga
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archive:bioinformatic_tools:sga [2011/06/08 16:30] eyliaw |
archive:bioinformatic_tools:sga [2011/06/08 23:50] karplus [Installation] |
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| * Like BWA, it uses the FM-index, which is a compressed method of inferring the suffix array. | * 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 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. | + | * 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" | ||
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| + | 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! | ||
archive/bioinformatic_tools/sga.txt · Last modified: 2015/07/28 06:26 by ceisenhart
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