SoftSearch:

 --SoftSearch is a tools that uses soft-masked reads and discordant read pairs to identify structural variation(SV) in 
   illumina next-generation sequencing data. 
 --It is a Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations.
 --Breakpoint is a place or time at which an interruption or change is made.
 --SoftSearch requires only two inputs: a BAM file of aligned reads and fasta file of the genome to which the reads were aligned.

 Google Code Link:
 
		https://code.google.com/p/softsearch/
		
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Pre-Requirement:

 -Perl
 -Bedtools  
 -SamTools
   Must have an entry in environment variable
    
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How To Selecte fasta file from Database (Additional Configuration):

 --Select fasta_indexes.loc file for that go to shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
   8578d978014c/softsearch/tool-data/

 --open the fasta_indexes.loc file and make changes like

        <unique_build_id>	<dbkey>	<display_name>	<file_base_path>

        eg: hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa

 --open shed_tool_data_table_conf.xml file and add following.

   	<tables>
    <table name="fasta_indexes" comment_char="#">
      	    <columns>value, dbkey, name, path</columns>
       	    <file path="/path/to/fasta_indexes.loc" />
  	    </table>
</tables>

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Authors:

   ResearchDx
   http://researchdx.com
   
   Plus91 Technologies Private Limited
   http://www.plus91.in/