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SoftSearch:

 --SoftSearch is a tool that uses soft-masked reads and discordant read pairs to identify structural variants(SV) in 
   Illumina paired-end next-generation sequencing data. 
 --Using Soft Clipped reads in which one part of the read maps to the reference genome but the other part does not SoftSearch 
   can identify and call SVs including deletions, insertions, translocations, inversions, and tandem duplications
 --SoftSearch requires two inputs: a BAM file of aligned reads and fasta file of the reference 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 be accessible from the PATH environment variable
    
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How To Select fasta file from Database (Additional Configuration):

 --A fasta_indexes.loc file must be located in shed_tools/toolshed.g2.bx.psu.edu/repos/plus91-technologies/softsearch/
   8578d978014c/softsearch/tool-data/

 --open the fasta_indexes.loc file and add an entry according to the example below

        <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 the 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/