GUSTAF uses SeqAns STELLAR to find splits as local matches on different strands or chromosomes. Criteria and penalties to chain these matches can be specified. Output file contains the breakpoints along the best chain.
The genome file is used as database input, the read file as query input.
All STELLAR options are supported. See STELLAR documentation for STELLAR parameters and options.
(c) 2011-2012 by Kathrin Trappe
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