Name: gustaf
Author: Kathrin Trappe <kathrin.trappe@fu-berlin.de>
Maintainer: Kathrin Trappe <kathrin.trappe@fu-berlin.de>
License: GPL v3
Copyright: 2011-2013, FU Berlin
Status: under development
Description: Calculates breakpoints of NGS reads having one or multiple split points.
 Given a reference sequence and one or multiple read sequences, Gustaf uses
 Stellar to partial read alignments. Compatible partial alignments are
 identified, and a split-read graph storing all compatibility information
 is constructed for each read.
 .
 Vertices in the graph represent partial alignments, edges represent
 possible split positions. Using an exact dynamic programming approach, we
 refine the alignments around possible split positions to determine precise
 breakpoint locations at single-nucleotide level. We use a DAG shortest path
 algorithm to determine the best combination of refined alignments, and report
 those breakpoints supported by multiple reads.

